log started: Tue Jun 9 11:48:33 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > source leaprc.ff03 ----- Source: /soft/amber10/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber10/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Tue Jun 9 11:48:40 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff ZNA.lib Loading library: ./ZNA.lib Loading: ZNA > loadamberparams frcmod.zna Loading parameters: ./frcmod.zna Reading force field modification type file (frcmod) Reading title: This frcmod file is for ZNA (zinc 2+ ion). (UNKNOWN ATOM TYPE: ZNA) > loadamberparams bzim.frcmod Loading parameters: ./bzim.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep bzim.prepin Loading Prep file: ./bzim.prepin Loaded UNIT: ABI > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT ZNA frcmod03 gaff parm99 > edit ABI Unit Editor: > check ABI Unit Editor: Checking 'ABI'.... Unit Editor: Checking parameters for unit 'ABI'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: Unit is OK. > bzim=loadpdb "c2k_bzim.pdb" Loading PDB file: ./c2k_bzim.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIS, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIS, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/beginning, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Created a new atom named: CA within residue: .R Added missing heavy atom: .R.A Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: CA within residue: .R Added missing heavy atom: .R.A Starting new chain with ZNA total atoms in file: 1647 Leap added 1620 missing atoms according to residue templates: 2 Heavy 1618 H / lone pairs The file contained 2 atoms not in residue templates > savepdb bzim c2k_bzim_xleap.pdb Writing pdb file: c2k_bzim_xleap.pdb > bzim1=loadpdb "c2k_bzim.pdb" Loading PDB file: ./c2k_bzim.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/beginning, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Created a new atom named: CA within residue: .R Added missing heavy atom: .R.A Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: CA within residue: .R Starting new chain with ZNA total atoms in file: 1648 Leap added 1619 missing atoms according to residue templates: 1 Heavy 1618 H / lone pairs The file contained 2 atoms not in residue templates > savepdb bzim1 c2k_bzimxleap.pdb Writing pdb file: c2k_bzimxleap.pdb > bzim2=loadpdb "c2k_bzimxleap.pdb" Loading PDB file: ./c2k_bzimxleap.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Created a new atom named: CA within residue: .R Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: CA within residue: .R total atoms in file: 3267 The file contained 2 atoms not in residue templates > bzim3=loadpdb "c2k_bzimxleap.pdb" Loading PDB file: ./c2k_bzimxleap.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME total atoms in file: 3265 > savepdb bzim3 c2k_bzimxleap.pdb Writing pdb file: c2k_bzimxleap.pdb > addions bzim3 Na+ 0 addIons: 1st Ion & target are the same charge: can't neutralize. > addions bzim3 Cl- 0 10 Cl- ions required to neutralize. Adding 10 counter ions to "bzim3" using 1A grid Total solute charge: 10.00 Max atom radius: 2.00 Grid extends from solute vdw + 5.49 to 11.49 Box: enclosing: 7.39 -14.11 9.62 73.66 44.36 82.51 sized: 135.39 113.89 137.62 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 2.69% of box, grid points 56322 (no solvent present) Calculating grid charges charges: 16 sec Placed Cl- in bzim3 at (45.39, 30.89, 45.62). Placed Cl- in bzim3 at (26.39, 21.89, 21.62). Placed Cl- in bzim3 at (28.39, -3.11, 36.62). Placed Cl- in bzim3 at (64.39, 10.89, 48.62). Placed Cl- in bzim3 at (24.39, 7.89, 61.62). Placed Cl- in bzim3 at (43.39, 28.89, 22.62). Placed Cl- in bzim3 at (49.39, 21.89, 71.62). Placed Cl- in bzim3 at (18.39, 2.89, 41.62). Placed Cl- in bzim3 at (46.39, -6.11, 47.62). Placed Cl- in bzim3 at (27.39, 29.89, 31.62). Done adding ions. > solvateoct bzim3 TIP3PBOX 8.0 Scaling up box by a factor of 1.304668 to meet diagonal cut criterion Solute vdw bounding box: 49.719 41.773 56.615 Total bounding box for atom centers: 77.490 77.490 77.490 (box expansion for 'iso' is 35.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 241771.494 A^3 (oct) Total mass 127191.786 amu, Density 0.874 g/cc Added 5727 residues. > saveamberparm bzim3 c2k_bzim.parm c2k_bzim.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for c2-hn-nh-hn atoms are: C7 H5 N2 H7 ** Warning: No sp2 improper torsion term for hn-hn-nh-c2 atoms are: H11 H12 N1 C7 old PREP-specified impropers: : C1 N1 C7 N2 : C7 C2 C1 C6 : C5 C1 C6 H6 : C2 C4 C3 H3 : C3 C5 C4 N3 : C4 C6 C5 N4 : C8 C5 N4 H4 : H8 N4 C8 N3 total 644 improper torsions applied 8 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 5727 ) (no restraints) > quit Quit log started: Wed Jun 10 08:57:16 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > source leaprc.ff03 ----- Source: /soft/amber10/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber10/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Wed Jun 10 08:57:24 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff ZNA.lib Loading library: ./ZNA.lib Loading: ZNA > loadamberparams frcmod.zna Loading parameters: ./frcmod.zna Reading force field modification type file (frcmod) Reading title: This frcmod file is for ZNA (zinc 2+ ion). (UNKNOWN ATOM TYPE: ZNA) > loadamberparams bzim.frcmod Loading parameters: ./bzim.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep bzim.prepin Loading Prep file: ./bzim.prepin Loaded UNIT: ABI > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT ZNA frcmod03 gaff parm99 > edit ABI Unit Editor: > check ABI Unit Editor: Checking 'ABI'.... Unit Editor: Checking parameters for unit 'ABI'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: Unit is OK. > bzim=loadpdb "c2k_bzim.pdb" Loading PDB file: ./c2k_bzim.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIS, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIS, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Added missing heavy atom: .R.A Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Added missing heavy atom: .R.A Created a new atom named: ZN within residue: .R Added missing heavy atom: .R.A Created a new atom named: ZN within residue: .R Added missing heavy atom: .R.A total atoms in file: 1645 Leap added 1620 missing atoms according to residue templates: 4 Heavy 1616 H / lone pairs The file contained 2 atoms not in residue templates > bzim1=loadpdb "c2k_bzim.pdb" Loading PDB file: ./c2k_bzim.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIS, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIS, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Added missing heavy atom: .R.A Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Added missing heavy atom: .R.A total atoms in file: 1645 Leap added 1618 missing atoms according to residue templates: 2 Heavy 1616 H / lone pairs > savepdb bzim1 c2k_bzim_xleap.pdb Writing pdb file: c2k_bzim_xleap.pdb > bzim2=loadpdb "c2k_bzim_xleap.pdb" Loading PDB file: ./c2k_bzim_xleap.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME total atoms in file: 3263 > saveamberparm bzim1 c2k_bzim1.prmtop c2k_bzim1.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 10.000000 is not zero. WARNING: The perturbed charge: 10.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for ce-hn-nh-hn atoms are: C7 H21 N2 H22 old PREP-specified impropers: : C1 N1 C7 N2 : C6 C2 C1 C7 : C5 C1 C6 H6 : C3 C1 C2 H2 : C2 C4 C3 H3 : C3 C5 C4 N3 : C6 C4 C5 N4 : C5 C8 N4 H4 : H8 N4 C8 N3 total 645 improper torsions applied 9 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > addions bzim1 Cl- 0 10 Cl- ions required to neutralize. Adding 10 counter ions to "bzim1" using 1A grid Total solute charge: 10.00 Max atom radius: 2.00 Grid extends from solute vdw + 5.49 to 11.49 Box: enclosing: 7.39 -14.11 9.62 73.66 44.35 82.51 sized: 135.39 113.89 137.62 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 0 sec Volume = 2.69% of box, grid points 56319 (no solvent present) Calculating grid charges charges: 18 sec Placed Cl- in bzim1 at (45.39, 30.89, 45.62). Placed Cl- in bzim1 at (26.39, 21.89, 21.62). Placed Cl- in bzim1 at (28.39, -3.11, 36.62). Placed Cl- in bzim1 at (64.39, 10.89, 48.62). Placed Cl- in bzim1 at (24.39, 7.89, 61.62). Placed Cl- in bzim1 at (43.39, 28.89, 22.62). Placed Cl- in bzim1 at (49.39, 21.89, 71.62). Placed Cl- in bzim1 at (18.39, 2.89, 41.62). Placed Cl- in bzim1 at (46.39, -6.11, 47.62). Placed Cl- in bzim1 at (27.39, 29.89, 31.62). Done adding ions. > solvateoct bzim1 TIP3PBOX 8.0 Scaling up box by a factor of 1.304699 to meet diagonal cut criterion Solute vdw bounding box: 49.743 41.776 56.595 Total bounding box for atom centers: 77.470 77.470 77.470 (box expansion for 'iso' is 35.6%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 241589.537 A^3 (oct) Total mass 127117.706 amu, Density 0.874 g/cc Added 5723 residues. > saveamberparm bzim1 c2k_bzim1.prmtop c2k_bzim1.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for ce-hn-nh-hn atoms are: C7 H21 N2 H22 old PREP-specified impropers: : C1 N1 C7 N2 : C6 C2 C1 C7 : C5 C1 C6 H6 : C3 C1 C2 H2 : C2 C4 C3 H3 : C3 C5 C4 N3 : C6 C4 C5 N4 : C5 C8 N4 H4 : H8 N4 C8 N3 total 645 improper torsions applied 9 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 5723 ) (no restraints) > quit Quit log started: Fri Jun 12 13:02:14 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > loadamberparams bzim_correct.frcmod Loading parameters: ./bzim_correct.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep bzimcorrect.prepin Could not open file bzimcorrect.prepin: not found > loadamberprep bzim_correct.prepin Loading Prep file: ./bzim_correct.prepin Loaded UNIT: ABI > list ABI gaff > desc ABi STRING (with no reference): 'ABi' > desc ABI UNIT name: ABI Head atom: .R.A Tail atom: .R.A Contents: R > desc ABI.1.A STRING (with no reference): 'ABI.1.A' > desc ABI.1.C STRING (with no reference): 'ABI.1.C' > desc ABI.1.N1 ATOM Name: N1 Type: n2 Charge: -0.8299 Polarization: 0.0000 Element: N Atom flags: (decimal 131072 hex 0x20000) posfxd n posblt n posdrwn n selected n pert n notdisp n touched n posknwn Y internal n needsmin n needsbuild n Atom position: 3.536914, 1.422858, -0.000002 Atom velocity: 0.000000, 0.000000, 0.000000 Bonded to .R.A

by a single bond. Bonded to .R.A by a single bond. > nedit ABI ERROR: syntax error > edit ABI Unit Editor: > check ABI Unit Editor: Checking 'ABI'.... Unit Editor: Checking parameters for unit 'ABI'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: Unit is OK. > quit Quit log started: Mon Jun 15 14:05:25 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > source leaprc.ff03 ----- Source: /soft/amber10/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber10/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Mon Jun 15 14:05:33 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff znb_ula.off Loading library: ./znb_ula.off Loading: ZNB > loadamberparams zinc_ula.params Loading parameters: ./zinc_ula.params Reading force field modification type file (frcmod) Reading title: Amber Force Field Parameters for the Tetrahedron-Shaped Zinc Divalent Cation (UNKNOWN ATOM TYPE: DZ) > loadamberparams bzim_correct.frcmod Loading parameters: ./bzim_correct.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep bzim_correct.prepin Loading Prep file: ./bzim_correct.prepin Loaded UNIT: ABI > test=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) Unknown residue: ZNA number: 225 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 226: ZNA, Terminal/last, was not found in name map.) Unknown residue: ZNA number: 226 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Creating new UNIT for residue: ZNA sequence: 226 Created a new atom named: ZNA within residue: .R Creating new UNIT for residue: ZNA sequence: 227 Created a new atom named: ZNA within residue: .R total atoms in file: 3263 The file contained 2 atoms not in residue templates > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT ZNB frcmod03 gaff parm99 test > test1=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) (Residue 226: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A total atoms in file: 3262 Leap added 5 missing atoms according to residue templates: 1 Heavy 4 unknown element The file contained 1 atoms not in residue templates > test2=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) (Residue 226: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A total atoms in file: 3262 Leap added 5 missing atoms according to residue templates: 1 Heavy 4 unknown element The file contained 1 atoms not in residue templates > test3=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) (Residue 226: ZNB, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A total atoms in file: 3263 Leap added 10 missing atoms according to residue templates: 2 Heavy 8 unknown element The file contained 2 atoms not in residue templates > edit ZNB Unit Editor: > check ZNB Unit Editor: Checking 'ZNB'.... Unit Editor: WARNING: The unperturbed charge of the unit: 2.000000 is not zero. Unit Editor: WARNING: The perturbed charge: 2.000000 is not zero. Unit Editor: Checking parameters for unit 'ZNB'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: check: Warnings: 2 Unit Editor: Unit is OK. > test4=loadpdb "c2k_bzim_ula.pdb" Loading PDB file: ./c2k_bzim_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) Mapped residue ASN, term: Terminal/last, seq. number: 224 to: CASN. (Residue 225: ZNB, Terminal/last, was not found in name map.) (Residue 226: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - CASN Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 3261 Leap added 14 missing atoms according to residue templates: 8 Heavy 6 H / lone pairs > test5=loadpdb "c2k_bzim_ula.pdb" Loading PDB file: ./c2k_bzim_ula.pdb Enter zPdbReadScan from call depth 0. Warning: name change in pdb file residue 224 ; this residue is split into ASN and ZNB. 1 residues had naming warnings. There are split residues; residue sequence numbers will not correspond to those in the pdb. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) Mapped residue ASN, term: Terminal/last, seq. number: 223 to: CASN. (Residue 224: ZNB, Terminal/last, was not found in name map.) (Residue 225: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - CASN total atoms in file: 3261 > test6=loadpdb "c2k_bzim_ula.pdb" Loading PDB file: ./c2k_bzim_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) Mapped residue ASN, term: Terminal/last, seq. number: 223 to: CASN. (Residue 224: ZNB, Terminal/last, was not found in name map.) (Residue 225: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - CASN total atoms in file: 3261 > addions test6 Cl- 0 7 Cl- ions required to neutralize. Adding 7 counter ions to "test6" using 1A grid Total solute charge: 7.00 Max atom radius: 3.10 Grid extends from solute vdw + 4.94 to 12.04 Box: enclosing: 6.84 -14.66 9.07 74.20 69.44 83.06 sized: 134.84 113.34 137.07 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 3.67% of box, grid points 77031 (no solvent present) Calculating grid charges charges: 27 sec Placed Cl- in test6 at (35.84, 37.34, 36.07). Placed Cl- in test6 at (28.84, 0.34, 35.07). Placed Cl- in test6 at (25.84, 22.34, 23.07). Placed Cl- in test6 at (63.84, 11.34, 48.07). Placed Cl- in test6 at (26.84, 31.34, 39.07). Placed Cl- in test6 at (24.84, 8.34, 61.07). Placed Cl- in test6 at (48.84, 17.34, 75.08). Done adding ions. > solvateoct test6 TIP3PBOX 8.0 (using default radius 1.500000 for D4) (using default radius 1.500000 for D3) (using default radius 1.500000 for D2) (using default radius 1.500000 for D1) Scaling up box by a factor of 1.377176 to meet diagonal cut criterion Solute vdw bounding box: 48.392 62.326 58.561 Total bounding box for atom centers: 84.361 84.361 84.361 (box expansion for 'iso' is 25.4%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 (using default radius 1.500000 for D4) (using default radius 1.500000 for D3) (using default radius 1.500000 for D2) (using default radius 1.500000 for D1) Volume: 310990.263 A^3 (oct) Total mass 167413.836 amu, Density 0.894 g/cc Added 7970 residues. > saveamberparm test6 c2k_bzim_ula.prmtop c2k_bzim_ula.inpcrd Checking Unit. WARNING: There is a bond of 42.716979 angstroms between: ------- .R.A and .R.A -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 1-4: angle 3240 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3240 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3240 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3239 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3238 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3238 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3240 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3238 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3241 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3238 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3239 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3237 3240 duplicates bond ('triangular' bond) or angle ('square' bond) Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for ce-hn-nh-hn atoms are: C7 H21 N2 H22 old PREP-specified impropers: : C1 N1 C7 N2 : C6 C2 C1 C7 : C5 C1 C6 H6 : C3 C1 C2 H2 : C2 C4 C3 H3 : C3 C5 C4 N3 : C6 C4 C5 N4 : C5 C8 N4 H4 : H8 N4 C8 N3 total 644 improper torsions applied 9 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CASN 1 WAT 7970 ZNB 1 ) (no restraints) log started: Tue Jun 16 09:40:56 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > source leaprc.ff03 ----- Source: /soft/amber10/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber10/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Tue Jun 16 09:41:03 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff znb_ula.off Loading library: ./znb_ula.off Loading: ZNB > loadamberparams zinc_ula.params Loading parameters: ./zinc_ula.params Reading force field modification type file (frcmod) Reading title: Amber Force Field Parameters for the Tetrahedron-Shaped Zinc Divalent Cation (UNKNOWN ATOM TYPE: DZ) > loadamberparams bzim_correct.frcmod Loading parameters: ./bzim_correct.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > laodamberprep bzim_correct.prepin ERROR: syntax error > loadamberprep bzim_correct.prepin Loading Prep file: ./bzim_correct.prepin Loaded UNIT: ABI > test=loadpdb "c2k_bim_Zn_ula.pdb" Could not open file c2k_bim_Zn_ula.pdb: not found > test=loadpdb "c2k_bzbim_Zn_ula.pdb" Could not open file c2k_bzbim_Zn_ula.pdb: not found > test=loadpdb "c2k_bzim_Zn_ula.pdb" Loading PDB file: ./c2k_bzim_Zn_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ABI, Terminal/last, was not found in name map.) (Residue 226: ZNB, Terminal/last, was not found in name map.) Joining ACE - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - TYR Created a new atom named: HN within residue: .R Joining TYR - THR Created a new atom named: HN within residue: .R Joining THR - CYS Created a new atom named: HN within residue: .R Joining CYS - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - PRO Joining PRO - TYR Created a new atom named: HN within residue: .R Joining TYR - GLN Created a new atom named: HN within residue: .R Joining GLN - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - TYR Created a new atom named: HN within residue: .R Joining TYR - HIE Created a new atom named: HN within residue: .R Joining HIE - PHE Created a new atom named: HN within residue: .R Joining PHE - CYS Created a new atom named: HN within residue: .R Joining CYS - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - ASN Created a new atom named: HN within residue: .R Joining ASN - SER Created a new atom named: HN within residue: .R Joining SER - GLN Created a new atom named: HN within residue: .R Joining GLN - TRP Created a new atom named: HN within residue: .R Joining TRP - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - ALA Created a new atom named: HN within residue: .R Joining ALA - HIE Created a new atom named: HN within residue: .R Joining HIE - CYS Created a new atom named: HN within residue: .R Joining CYS - TYR Created a new atom named: HN within residue: .R Joining TYR - LYS Created a new atom named: HN within residue: .R Joining LYS - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - GLN Created a new atom named: HN within residue: .R Joining GLN - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HN within residue: .R Joining ARG - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - GLU Created a new atom named: HN within residue: .R Joining GLU - ASP Created a new atom named: HN within residue: .R Joining ASP - ASN Created a new atom named: HN within residue: .R Joining ASN - ILE Created a new atom named: HN within residue: .R Joining ILE - ASN Created a new atom named: HN within residue: .R Joining ASN - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ASN Created a new atom named: HN within residue: .R Joining ASN - GLU Created a new atom named: HN within residue: .R Joining GLU - GLN Created a new atom named: HN within residue: .R Joining GLN - PHE Created a new atom named: HN within residue: .R Joining PHE - ILE Created a new atom named: HN within residue: .R Joining ILE - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - LYS Created a new atom named: HN within residue: .R Joining LYS - SER Created a new atom named: HN within residue: .R Joining SER - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - HIE Created a new atom named: HN within residue: .R Joining HIE - PRO Joining PRO - SER Created a new atom named: HN within residue: .R Joining SER - TYR Created a new atom named: HN within residue: .R Joining TYR - ASN Created a new atom named: HN within residue: .R Joining ASN - SER Created a new atom named: HN within residue: .R Joining SER - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - ASN Created a new atom named: HN within residue: .R Joining ASN - ASP Created a new atom named: HN within residue: .R Joining ASP - ILE Created a new atom named: HN within residue: .R Joining ILE - MET Created a new atom named: HN within residue: .R Joining MET - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HN within residue: .R Joining LYS - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - SER Created a new atom named: HN within residue: .R Joining SER - ARG Created a new atom named: HN within residue: .R Joining ARG - VAL Created a new atom named: HN within residue: .R Joining VAL - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - ILE Created a new atom named: HN within residue: .R Joining ILE - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - PRO Joining PRO - THR Created a new atom named: HN within residue: .R Joining THR - SER Created a new atom named: HN within residue: .R Joining SER - CYS Created a new atom named: HN within residue: .R Joining CYS - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - THR Created a new atom named: HN within residue: .R Joining THR - GLN Created a new atom named: HN within residue: .R Joining GLN - CYS Created a new atom named: HN within residue: .R Joining CYS - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - TRP Created a new atom named: HN within residue: .R Joining TRP - GLY Created a new atom named: HN within residue: .R Joining GLY - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - LYS Created a new atom named: HN within residue: .R Joining LYS - SER Created a new atom named: HN within residue: .R Joining SER - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - THR Created a new atom named: HN within residue: .R Joining THR - SER Created a new atom named: HN within residue: .R Joining SER - TYR Created a new atom named: HN within residue: .R Joining TYR - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - CYS Created a new atom named: HN within residue: .R Joining CYS - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - ALA Created a new atom named: HN within residue: .R Joining ALA - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - LEU Created a new atom named: HN within residue: .R Joining LEU - SER Created a new atom named: HN within residue: .R Joining SER - ASP Created a new atom named: HN within residue: .R Joining ASP - SER Created a new atom named: HN within residue: .R Joining SER - SER Created a new atom named: HN within residue: .R Joining SER - CYS Created a new atom named: HN within residue: .R Joining CYS - LYS Created a new atom named: HN within residue: .R Joining LYS - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - TYR Created a new atom named: HN within residue: .R Joining TYR - PRO Joining PRO - GLY Created a new atom named: HN within residue: .R Joining GLY - GLN Created a new atom named: HN within residue: .R Joining GLN - ILE Created a new atom named: HN within residue: .R Joining ILE - THR Created a new atom named: HN within residue: .R Joining THR - SER Created a new atom named: HN within residue: .R Joining SER - ASN Created a new atom named: HN within residue: .R Joining ASN - MET Created a new atom named: HN within residue: .R Joining MET - PHE Created a new atom named: HN within residue: .R Joining PHE - CYS Created a new atom named: HN within residue: .R Joining CYS - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - LYS Created a new atom named: HN within residue: .R Joining LYS - ASP Created a new atom named: HN within residue: .R Joining ASP - SER Created a new atom named: HN within residue: .R Joining SER - CYS Created a new atom named: HN within residue: .R Joining CYS - GLN Created a new atom named: HN within residue: .R Joining GLN - GLY Created a new atom named: HN within residue: .R Joining GLY - ASP Created a new atom named: HN within residue: .R Joining ASP - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - CYS Created a new atom named: HN within residue: .R Joining CYS - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - LYS Created a new atom named: HN within residue: .R Joining LYS - LEU Created a new atom named: HN within residue: .R Joining LEU - GLN Created a new atom named: HN within residue: .R Joining GLN - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - TRP Created a new atom named: HN within residue: .R Joining TRP - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - CYS Created a new atom named: HN within residue: .R Joining CYS - ALA Created a new atom named: HN within residue: .R Joining ALA - GLN Created a new atom named: HN within residue: .R Joining GLN - LYS Created a new atom named: HN within residue: .R Joining LYS - ASN Created a new atom named: HN within residue: .R Joining ASN - LYS Created a new atom named: HN within residue: .R Joining LYS - PRO Joining PRO - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - TYR Created a new atom named: HN within residue: .R Joining TYR - THR Created a new atom named: HN within residue: .R Joining THR - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - CYS Created a new atom named: HN within residue: .R Joining CYS - ASN Created a new atom named: HN within residue: .R Joining ASN - TYR Created a new atom named: HN within residue: .R Joining TYR - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - TRP Created a new atom named: HN within residue: .R Joining TRP - ILE Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HN within residue: .R Joining LYS - GLN Created a new atom named: HN within residue: .R Joining GLN - THR Created a new atom named: HN within residue: .R Joining THR - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - ASN Created a new atom named: HN within residue: .R Joining ASN - NME Created a new atom named: ZN within residue: .R Added missing heavy atom: .R.A total atoms in file: 3266 Leap added 216 missing atoms according to residue templates: 1 Heavy 215 H / lone pairs The file contained 216 atoms not in residue templates Since added/missing = extra, there is a high probability of atoms with 'incorrect' names; you may want to use addPdbAtomMap to map these names, or change in file > test1=loadpdb "c2k_bzim_Zn_ula.pdb" Loading PDB file: ./c2k_bzim_Zn_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ABI, Terminal/last, was not found in name map.) (Residue 226: ZNB, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZN within residue: .R Added missing heavy atom: .R.A total atoms in file: 1650 Leap added 1617 missing atoms according to residue templates: 1 Heavy 1616 H / lone pairs The file contained 1 atoms not in residue templates > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT ZNB frcmod03 gaff parm99 test test1 > test2=loadpdb "c2k_bzim_Zn_ula.pdb" Loading PDB file: ./c2k_bzim_Zn_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ABI, Terminal/last, was not found in name map.) (Residue 226: ZNB, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A total atoms in file: 1650 Leap added 1617 missing atoms according to residue templates: 1 Heavy 1616 H / lone pairs The file contained 1 atoms not in residue templates > savepdb test2 test2_xleap.pdb Writing pdb file: test2_xleap.pdb > test3=loadpdb "c2k_bzim_Zn_ula.pdb" Loading PDB file: ./c2k_bzim_Zn_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ILE, term: Terminal/beginning, seq. number: 0 to: NILE. (Residue 1: VAL, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: TYR, Nonterminal, was not found in name map.) (Residue 5: THR, Nonterminal, was not found in name map.) (Residue 6: CYS, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: ALA, Nonterminal, was not found in name map.) (Residue 9: ASN, Nonterminal, was not found in name map.) (Residue 10: THR, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: TYR, Nonterminal, was not found in name map.) (Residue 14: GLN, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: SER, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: ASN, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: TYR, Nonterminal, was not found in name map.) (Residue 22: HIE, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: CYS, Nonterminal, was not found in name map.) (Residue 25: GLY, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: SER, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: ILE, Nonterminal, was not found in name map.) (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: SER, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: TRP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: ALA, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: HIE, Nonterminal, was not found in name map.) (Residue 40: CYS, Nonterminal, was not found in name map.) (Residue 41: TYR, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLY, Nonterminal, was not found in name map.) (Residue 45: ILE, Nonterminal, was not found in name map.) (Residue 46: GLN, Nonterminal, was not found in name map.) (Residue 47: VAL, Nonterminal, was not found in name map.) (Residue 48: ARG, Nonterminal, was not found in name map.) (Residue 49: LEU, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: GLU, Nonterminal, was not found in name map.) (Residue 52: ASP, Nonterminal, was not found in name map.) (Residue 53: ASN, Nonterminal, was not found in name map.) (Residue 54: ILE, Nonterminal, was not found in name map.) (Residue 55: ASN, Nonterminal, was not found in name map.) (Residue 56: VAL, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: GLU, Nonterminal, was not found in name map.) (Residue 59: GLY, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: GLN, Nonterminal, was not found in name map.) (Residue 63: PHE, Nonterminal, was not found in name map.) (Residue 64: ILE, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: ALA, Nonterminal, was not found in name map.) (Residue 67: SER, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: SER, Nonterminal, was not found in name map.) (Residue 70: ILE, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: HIE, Nonterminal, was not found in name map.) (Residue 73: PRO, Nonterminal, was not found in name map.) (Residue 74: SER, Nonterminal, was not found in name map.) (Residue 75: TYR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: SER, Nonterminal, was not found in name map.) (Residue 78: ASN, Nonterminal, was not found in name map.) (Residue 79: THR, Nonterminal, was not found in name map.) (Residue 80: LEU, Nonterminal, was not found in name map.) (Residue 81: ASN, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASP, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: ILE, Nonterminal, was not found in name map.) (Residue 88: LYS, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: LYS, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ALA, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: SER, Nonterminal, was not found in name map.) (Residue 95: LEU, Nonterminal, was not found in name map.) (Residue 96: ASN, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: VAL, Nonterminal, was not found in name map.) (Residue 100: ALA, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: PRO, Nonterminal, was not found in name map.) (Residue 106: THR, Nonterminal, was not found in name map.) (Residue 107: SER, Nonterminal, was not found in name map.) (Residue 108: CYS, Nonterminal, was not found in name map.) (Residue 109: ALA, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: ALA, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: GLN, Nonterminal, was not found in name map.) (Residue 115: CYS, Nonterminal, was not found in name map.) (Residue 116: LEU, Nonterminal, was not found in name map.) (Residue 117: ILE, Nonterminal, was not found in name map.) (Residue 118: SER, Nonterminal, was not found in name map.) (Residue 119: GLY, Nonterminal, was not found in name map.) (Residue 120: TRP, Nonterminal, was not found in name map.) (Residue 121: GLY, Nonterminal, was not found in name map.) (Residue 122: ASN, Nonterminal, was not found in name map.) (Residue 123: THR, Nonterminal, was not found in name map.) (Residue 124: LYS, Nonterminal, was not found in name map.) (Residue 125: SER, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: GLY, Nonterminal, was not found in name map.) (Residue 128: THR, Nonterminal, was not found in name map.) (Residue 129: SER, Nonterminal, was not found in name map.) (Residue 130: TYR, Nonterminal, was not found in name map.) (Residue 131: PRO, Nonterminal, was not found in name map.) (Residue 132: ASP, Nonterminal, was not found in name map.) (Residue 133: VAL, Nonterminal, was not found in name map.) (Residue 134: LEU, Nonterminal, was not found in name map.) (Residue 135: LYS, Nonterminal, was not found in name map.) (Residue 136: CYS, Nonterminal, was not found in name map.) (Residue 137: LEU, Nonterminal, was not found in name map.) (Residue 138: LYS, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ILE, Nonterminal, was not found in name map.) (Residue 142: LEU, Nonterminal, was not found in name map.) (Residue 143: SER, Nonterminal, was not found in name map.) (Residue 144: ASP, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: CYS, Nonterminal, was not found in name map.) (Residue 148: LYS, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: PRO, Nonterminal, was not found in name map.) (Residue 153: GLY, Nonterminal, was not found in name map.) (Residue 154: GLN, Nonterminal, was not found in name map.) (Residue 155: ILE, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: SER, Nonterminal, was not found in name map.) (Residue 158: ASN, Nonterminal, was not found in name map.) (Residue 159: MET, Nonterminal, was not found in name map.) (Residue 160: PHE, Nonterminal, was not found in name map.) (Residue 161: CYS, Nonterminal, was not found in name map.) (Residue 162: ALA, Nonterminal, was not found in name map.) (Residue 163: GLY, Nonterminal, was not found in name map.) (Residue 164: TYR, Nonterminal, was not found in name map.) (Residue 165: LEU, Nonterminal, was not found in name map.) (Residue 166: GLU, Nonterminal, was not found in name map.) (Residue 167: GLY, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: LYS, Nonterminal, was not found in name map.) (Residue 170: ASP, Nonterminal, was not found in name map.) (Residue 171: SER, Nonterminal, was not found in name map.) (Residue 172: CYS, Nonterminal, was not found in name map.) (Residue 173: GLN, Nonterminal, was not found in name map.) (Residue 174: GLY, Nonterminal, was not found in name map.) (Residue 175: ASP, Nonterminal, was not found in name map.) (Residue 176: SER, Nonterminal, was not found in name map.) (Residue 177: GLY, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: PRO, Nonterminal, was not found in name map.) (Residue 180: VAL, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: CYS, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: LYS, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: GLN, Nonterminal, was not found in name map.) (Residue 188: GLY, Nonterminal, was not found in name map.) (Residue 189: ILE, Nonterminal, was not found in name map.) (Residue 190: VAL, Nonterminal, was not found in name map.) (Residue 191: SER, Nonterminal, was not found in name map.) (Residue 192: TRP, Nonterminal, was not found in name map.) (Residue 193: GLY, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: GLY, Nonterminal, was not found in name map.) (Residue 196: CYS, Nonterminal, was not found in name map.) (Residue 197: ALA, Nonterminal, was not found in name map.) (Residue 198: GLN, Nonterminal, was not found in name map.) (Residue 199: LYS, Nonterminal, was not found in name map.) (Residue 200: ASN, Nonterminal, was not found in name map.) (Residue 201: LYS, Nonterminal, was not found in name map.) (Residue 202: PRO, Nonterminal, was not found in name map.) (Residue 203: GLY, Nonterminal, was not found in name map.) (Residue 204: VAL, Nonterminal, was not found in name map.) (Residue 205: TYR, Nonterminal, was not found in name map.) (Residue 206: THR, Nonterminal, was not found in name map.) (Residue 207: LYS, Nonterminal, was not found in name map.) (Residue 208: VAL, Nonterminal, was not found in name map.) (Residue 209: CYS, Nonterminal, was not found in name map.) (Residue 210: ASN, Nonterminal, was not found in name map.) (Residue 211: TYR, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: SER, Nonterminal, was not found in name map.) (Residue 214: TRP, Nonterminal, was not found in name map.) (Residue 215: ILE, Nonterminal, was not found in name map.) (Residue 216: LYS, Nonterminal, was not found in name map.) (Residue 217: GLN, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ILE, Nonterminal, was not found in name map.) (Residue 220: ALA, Nonterminal, was not found in name map.) (Residue 221: SER, Nonterminal, was not found in name map.) (Residue 222: ASN, Nonterminal, was not found in name map.) (Residue 223: NME, Terminal/last, was not found in name map.) (Residue 224: ABI, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) Joining NILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: ZNB within residue: .R Added missing heavy atom: .R.A total atoms in file: 1649 Leap added 1614 missing atoms according to residue templates: 1 Heavy 1613 H / lone pairs The file contained 1 atoms not in residue templates > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT ZNB frcmod03 gaff parm99 test test1 test2 test3 > desc ZNB UNIT name: Head atom: null Tail atom: null Contents: R > desc TNB.1 STRING (with no reference): 'TNB.1' > desc ZNB.1 RESIDUE name: ZNB RESIDUE sequence number: 1 RESIDUE PDB sequence number: 1 Type: undefined Connection atoms: Improper torsions: Contents: A A A A A > test4loadpdb "c2k_bzim_Zn_ula.pdb" ERROR: syntax error > test4=loadpdb "c2k_bzim_Zn_ula.pdb" Loading PDB file: ./c2k_bzim_Zn_ula.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ILE, term: Terminal/beginning, seq. number: 0 to: NILE. (Residue 1: VAL, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: TYR, Nonterminal, was not found in name map.) (Residue 5: THR, Nonterminal, was not found in name map.) (Residue 6: CYS, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: ALA, Nonterminal, was not found in name map.) (Residue 9: ASN, Nonterminal, was not found in name map.) (Residue 10: THR, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: TYR, Nonterminal, was not found in name map.) (Residue 14: GLN, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: SER, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: ASN, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: TYR, Nonterminal, was not found in name map.) (Residue 22: HIE, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: CYS, Nonterminal, was not found in name map.) (Residue 25: GLY, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: SER, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: ILE, Nonterminal, was not found in name map.) (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: SER, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: TRP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: ALA, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: HIE, Nonterminal, was not found in name map.) (Residue 40: CYS, Nonterminal, was not found in name map.) (Residue 41: TYR, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLY, Nonterminal, was not found in name map.) (Residue 45: ILE, Nonterminal, was not found in name map.) (Residue 46: GLN, Nonterminal, was not found in name map.) (Residue 47: VAL, Nonterminal, was not found in name map.) (Residue 48: ARG, Nonterminal, was not found in name map.) (Residue 49: LEU, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: GLU, Nonterminal, was not found in name map.) (Residue 52: ASP, Nonterminal, was not found in name map.) (Residue 53: ASN, Nonterminal, was not found in name map.) (Residue 54: ILE, Nonterminal, was not found in name map.) (Residue 55: ASN, Nonterminal, was not found in name map.) (Residue 56: VAL, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: GLU, Nonterminal, was not found in name map.) (Residue 59: GLY, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: GLN, Nonterminal, was not found in name map.) (Residue 63: PHE, Nonterminal, was not found in name map.) (Residue 64: ILE, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: ALA, Nonterminal, was not found in name map.) (Residue 67: SER, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: SER, Nonterminal, was not found in name map.) (Residue 70: ILE, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: HIE, Nonterminal, was not found in name map.) (Residue 73: PRO, Nonterminal, was not found in name map.) (Residue 74: SER, Nonterminal, was not found in name map.) (Residue 75: TYR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: SER, Nonterminal, was not found in name map.) (Residue 78: ASN, Nonterminal, was not found in name map.) (Residue 79: THR, Nonterminal, was not found in name map.) (Residue 80: LEU, Nonterminal, was not found in name map.) (Residue 81: ASN, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASP, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: ILE, Nonterminal, was not found in name map.) (Residue 88: LYS, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: LYS, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ALA, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: SER, Nonterminal, was not found in name map.) (Residue 95: LEU, Nonterminal, was not found in name map.) (Residue 96: ASN, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: VAL, Nonterminal, was not found in name map.) (Residue 100: ALA, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: PRO, Nonterminal, was not found in name map.) (Residue 106: THR, Nonterminal, was not found in name map.) (Residue 107: SER, Nonterminal, was not found in name map.) (Residue 108: CYS, Nonterminal, was not found in name map.) (Residue 109: ALA, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: ALA, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: GLN, Nonterminal, was not found in name map.) (Residue 115: CYS, Nonterminal, was not found in name map.) (Residue 116: LEU, Nonterminal, was not found in name map.) (Residue 117: ILE, Nonterminal, was not found in name map.) (Residue 118: SER, Nonterminal, was not found in name map.) (Residue 119: GLY, Nonterminal, was not found in name map.) (Residue 120: TRP, Nonterminal, was not found in name map.) (Residue 121: GLY, Nonterminal, was not found in name map.) (Residue 122: ASN, Nonterminal, was not found in name map.) (Residue 123: THR, Nonterminal, was not found in name map.) (Residue 124: LYS, Nonterminal, was not found in name map.) (Residue 125: SER, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: GLY, Nonterminal, was not found in name map.) (Residue 128: THR, Nonterminal, was not found in name map.) (Residue 129: SER, Nonterminal, was not found in name map.) (Residue 130: TYR, Nonterminal, was not found in name map.) (Residue 131: PRO, Nonterminal, was not found in name map.) (Residue 132: ASP, Nonterminal, was not found in name map.) (Residue 133: VAL, Nonterminal, was not found in name map.) (Residue 134: LEU, Nonterminal, was not found in name map.) (Residue 135: LYS, Nonterminal, was not found in name map.) (Residue 136: CYS, Nonterminal, was not found in name map.) (Residue 137: LEU, Nonterminal, was not found in name map.) (Residue 138: LYS, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ILE, Nonterminal, was not found in name map.) (Residue 142: LEU, Nonterminal, was not found in name map.) (Residue 143: SER, Nonterminal, was not found in name map.) (Residue 144: ASP, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: CYS, Nonterminal, was not found in name map.) (Residue 148: LYS, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: PRO, Nonterminal, was not found in name map.) (Residue 153: GLY, Nonterminal, was not found in name map.) (Residue 154: GLN, Nonterminal, was not found in name map.) (Residue 155: ILE, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: SER, Nonterminal, was not found in name map.) (Residue 158: ASN, Nonterminal, was not found in name map.) (Residue 159: MET, Nonterminal, was not found in name map.) (Residue 160: PHE, Nonterminal, was not found in name map.) (Residue 161: CYS, Nonterminal, was not found in name map.) (Residue 162: ALA, Nonterminal, was not found in name map.) (Residue 163: GLY, Nonterminal, was not found in name map.) (Residue 164: TYR, Nonterminal, was not found in name map.) (Residue 165: LEU, Nonterminal, was not found in name map.) (Residue 166: GLU, Nonterminal, was not found in name map.) (Residue 167: GLY, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: LYS, Nonterminal, was not found in name map.) (Residue 170: ASP, Nonterminal, was not found in name map.) (Residue 171: SER, Nonterminal, was not found in name map.) (Residue 172: CYS, Nonterminal, was not found in name map.) (Residue 173: GLN, Nonterminal, was not found in name map.) (Residue 174: GLY, Nonterminal, was not found in name map.) (Residue 175: ASP, Nonterminal, was not found in name map.) (Residue 176: SER, Nonterminal, was not found in name map.) (Residue 177: GLY, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: PRO, Nonterminal, was not found in name map.) (Residue 180: VAL, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: CYS, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: LYS, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: GLN, Nonterminal, was not found in name map.) (Residue 188: GLY, Nonterminal, was not found in name map.) (Residue 189: ILE, Nonterminal, was not found in name map.) (Residue 190: VAL, Nonterminal, was not found in name map.) (Residue 191: SER, Nonterminal, was not found in name map.) (Residue 192: TRP, Nonterminal, was not found in name map.) (Residue 193: GLY, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: GLY, Nonterminal, was not found in name map.) (Residue 196: CYS, Nonterminal, was not found in name map.) (Residue 197: ALA, Nonterminal, was not found in name map.) (Residue 198: GLN, Nonterminal, was not found in name map.) (Residue 199: LYS, Nonterminal, was not found in name map.) (Residue 200: ASN, Nonterminal, was not found in name map.) (Residue 201: LYS, Nonterminal, was not found in name map.) (Residue 202: PRO, Nonterminal, was not found in name map.) (Residue 203: GLY, Nonterminal, was not found in name map.) (Residue 204: VAL, Nonterminal, was not found in name map.) (Residue 205: TYR, Nonterminal, was not found in name map.) (Residue 206: THR, Nonterminal, was not found in name map.) (Residue 207: LYS, Nonterminal, was not found in name map.) (Residue 208: VAL, Nonterminal, was not found in name map.) (Residue 209: CYS, Nonterminal, was not found in name map.) (Residue 210: ASN, Nonterminal, was not found in name map.) (Residue 211: TYR, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: SER, Nonterminal, was not found in name map.) (Residue 214: TRP, Nonterminal, was not found in name map.) (Residue 215: ILE, Nonterminal, was not found in name map.) (Residue 216: LYS, Nonterminal, was not found in name map.) (Residue 217: GLN, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ILE, Nonterminal, was not found in name map.) (Residue 220: ALA, Nonterminal, was not found in name map.) (Residue 221: SER, Nonterminal, was not found in name map.) (Residue 222: ASN, Nonterminal, was not found in name map.) (Residue 223: NME, Terminal/last, was not found in name map.) (Residue 224: ABI, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) Joining NILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME total atoms in file: 1649 Leap added 1613 missing atoms according to residue templates: 1613 H / lone pairs > savepdb test4 test4_xleap.pdb Writing pdb file: test4_xleap.pdb Converting N-terminal residue name to PDB format: NILE -> ILE > addions test4 Cl- 0 9 Cl- ions required to neutralize. Adding 9 counter ions to "test4" using 1A grid Total solute charge: 9.00 Max atom radius: 3.10 Grid extends from solute vdw + 5.32 to 12.42 Box: enclosing: 6.46 -15.04 8.69 74.59 45.28 83.44 sized: 134.46 112.96 136.69 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 3.40% of box, grid points 71345 (no solvent present) Calculating grid charges charges: 25 sec Placed Cl- in test4 at (44.46, 30.96, 45.69). Placed Cl- in test4 at (28.46, -3.04, 36.69). Placed Cl- in test4 at (26.46, 21.96, 21.69). Placed Cl- in test4 at (64.46, 10.96, 47.69). Placed Cl- in test4 at (24.46, 7.96, 60.69). Placed Cl- in test4 at (49.46, 19.96, 73.69). Placed Cl- in test4 at (43.46, 27.96, 21.69). Placed Cl- in test4 at (18.46, 2.96, 40.69). Placed Cl- in test4 at (45.46, -4.04, 44.69). Done adding ions. > solvateoct test4 TIP3PBOX 8.0 (using default radius 1.500000 for D4) (using default radius 1.500000 for D3) (using default radius 1.500000 for D2) (using default radius 1.500000 for D1) Scaling up box by a factor of 1.271836 to meet diagonal cut criterion Solute vdw bounding box: 49.771 39.934 58.598 Total bounding box for atom centers: 78.947 78.947 78.947 (box expansion for 'iso' is 47.4%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 (using default radius 1.500000 for D4) (using default radius 1.500000 for D3) (using default radius 1.500000 for D2) (using default radius 1.500000 for D1) Volume: 255494.322 A^3 (oct) Total mass 135515.392 amu, Density 0.881 g/cc Added 6197 residues. > saveamberparm test4 c2k_bzim_ula.prmtop c2k_bzim_ula.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 1-4: angle 3261 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3261 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3261 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3260 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3259 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3259 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3261 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3259 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3262 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3259 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3260 duplicates bond ('triangular' bond) or angle ('square' bond) 1-4: angle 3258 3261 duplicates bond ('triangular' bond) or angle ('square' bond) Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for ce-hn-nh-hn atoms are: C7 H21 N2 H22 old PREP-specified impropers: : C1 N1 C7 N2 : C6 C2 C1 C7 : C5 C1 C6 H6 : C3 C1 C2 H2 : C2 C4 C3 H3 : C3 C5 C4 N3 : C6 C4 C5 N4 : C5 C8 N4 H4 : H8 N4 C8 N3 total 643 improper torsions applied 9 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected NILE 1 WAT 6197 ZNB 1 ) (no restraints) > quit Quit > edit ABI Unit Editor: > check ABI Unit Editor: Checking 'ABI'.... Unit Editor: Checking parameters for unit 'ABI'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: Unit is OK. > quit Quit log started: Wed Jun 24 13:19:25 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > source leaprc.f03 Could not open file leaprc.f03: not found > source leaprc.ff03 ----- Source: /soft/amber10/dat/leap/cmd/leaprc.ff03 ----- Source of /soft/amber10/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Wed Jun 24 13:19:43 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadamberparams bzim_wrong.frcmod Loading parameters: ./bzim_wrong.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep /bzim_wrong.prepin Could not open file /bzim_wrong.prepin: No such file or directory > loadamberprep bzim_wrong.prepin Loading Prep file: ./bzim_wrong.prepin Loaded UNIT: ABI > list ABI ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX TP3 TP4 TP5 TPF TRP TYR VAL WAT frcmod03 gaff parm99 > edit ABI > loadoff ZNA.lib Loading library: ./ZNA.lib Loading: ZNA > loadamberparams zna.frcmod Could not open file zna.frcmod: not found > loadamberparams frcmod.zna Loading parameters: ./frcmod.zna Reading force field modification type file (frcmod) Reading title: This frcmod file is for ZNA (zinc 2+ ion). (UNKNOWN ATOM TYPE: ZNA) > test=loadpdb "c2k_bzim_wrong.pdb" Loading PDB file: ./c2k_bzim_wrong.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Created a new atom named: H11 within residue: .R Created a new atom named: H12 within residue: .R Created a new atom named: H21 within residue: .R Created a new atom named: H22 within residue: .R total atoms in file: 3265 Leap added 4 missing atoms according to residue templates: 4 H / lone pairs The file contained 4 atoms not in residue templates Since added/missing = extra, there is a high probability of atoms with 'incorrect' names; you may want to use addPdbAtomMap to map these names, or change in file > edit test Unit Editor: > check test Unit Editor: Checking 'test'.... Unit Editor: WARNING: The unperturbed charge of the unit: 10.000100 is not zero. Unit Editor: WARNING: The perturbed charge: 10.000100 is not zero. Unit Editor: FATAL: Atom .R.A does not have a type. Unit Editor: FATAL: Atom .R.A does not have a type. Unit Editor: FATAL: Atom .R.A does not have a type. Unit Editor: FATAL: Atom .R.A does not have a type. Unit Editor: Warning: Close contact of 1.608569 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.959593 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.919411 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.771049 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.006714 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.461992 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.856148 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.104739 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.078677 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.638010 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.982453 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.990506 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.679819 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.202763 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.183734 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.446350 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.693203 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.509214 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.687266 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.262243 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.957138 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.044286 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.594164 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.981931 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.000000 angstroms between .R.A

and .R.A Unit Editor: Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.188533 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.188554 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 0.000000 angstroms between .R.A

and .R.A Unit Editor: Warning: Close contact of 0.000000 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.019819 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.020411 angstroms between .R.A and .R.A Unit Editor: Checking parameters for unit 'test'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: check: Errors: 4 Warnings: 34 > quit Quit log started: Thu Jun 25 11:10:30 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /soft/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /soft/amber10/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /soft/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /soft/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /soft/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_aminoct94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /soft/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff all_amino03.lib Loading library: /soft/amber10/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /soft/amber10/dat/leap/cmd/leaprc.gaff ----- Source of /soft/amber10/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Thu Jun 25 11:10:38 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /soft/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > loadoff ZNA.lib Loading library: ./ZNA.lib Loading: ZNA > loadamberparams frcmod.zna Loading parameters: ./frcmod.zna Reading force field modification type file (frcmod) Reading title: This frcmod file is for ZNA (zinc 2+ ion). (UNKNOWN ATOM TYPE: ZNA) > loadamberparams bzim_correct.frcmod Loading parameters: ./bzim_correct.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep bzim_correct.prepin Loading Prep file: ./bzim_correct.prepin Loaded UNIT: ABI > test=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNB, Terminal/last, was not found in name map.) Unknown residue: ZNB number: 225 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 226: ZNB, Terminal/last, was not found in name map.) Unknown residue: ZNB number: 226 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME Creating new UNIT for residue: ZNB sequence: 226 Created a new atom named: ZNB within residue: .R Creating new UNIT for residue: ZNB sequence: 227 Created a new atom named: ZNB within residue: .R total atoms in file: 3263 The file contained 2 atoms not in residue templates > test1=loadpdb "c2k_bzim_correct.pdb" Loading PDB file: ./c2k_bzim_correct.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: VAL, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: TYR, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: CYS, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ASN, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: TYR, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: VAL, Nonterminal, was not found in name map.) (Residue 17: SER, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: CYS, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: ILE, Nonterminal, was not found in name map.) (Residue 31: ASN, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: GLN, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: HIE, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: GLN, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: ILE, Nonterminal, was not found in name map.) (Residue 56: ASN, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: SER, Nonterminal, was not found in name map.) (Residue 71: ILE, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: ASN, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: LEU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ASN, Nonterminal, was not found in name map.) (Residue 84: ASP, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: LYS, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: SER, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ASN, Nonterminal, was not found in name map.) (Residue 98: SER, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: SER, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: PRO, Nonterminal, was not found in name map.) (Residue 107: THR, Nonterminal, was not found in name map.) (Residue 108: SER, Nonterminal, was not found in name map.) (Residue 109: CYS, Nonterminal, was not found in name map.) (Residue 110: ALA, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: CYS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: TRP, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: THR, Nonterminal, was not found in name map.) (Residue 125: LYS, Nonterminal, was not found in name map.) (Residue 126: SER, Nonterminal, was not found in name map.) (Residue 127: SER, Nonterminal, was not found in name map.) (Residue 128: GLY, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: TYR, Nonterminal, was not found in name map.) (Residue 132: PRO, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: LYS, Nonterminal, was not found in name map.) (Residue 137: CYS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: LYS, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: SER, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: SER, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: ALA, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: GLY, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: ASN, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: CYS, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: GLY, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: LEU, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: GLN, Nonterminal, was not found in name map.) (Residue 175: GLY, Nonterminal, was not found in name map.) (Residue 176: ASP, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: GLY, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: CYS, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: GLN, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: CYS, Nonterminal, was not found in name map.) (Residue 198: ALA, Nonterminal, was not found in name map.) (Residue 199: GLN, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ASN, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: LYS, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: CYS, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: TRP, Nonterminal, was not found in name map.) (Residue 216: ILE, Nonterminal, was not found in name map.) (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: THR, Nonterminal, was not found in name map.) (Residue 220: ILE, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: NME, Terminal/last, was not found in name map.) (Residue 225: ZNA, Terminal/last, was not found in name map.) (Residue 226: ZNA, Terminal/last, was not found in name map.) (Residue 227: ABI, Terminal/last, was not found in name map.) Joining ACE - ILE Joining ILE - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - GLY Joining GLY - TYR Joining TYR - HIE Joining HIE - PHE Joining PHE - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - SER Joining SER - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - SER Joining SER - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - VAL Joining VAL - SER Joining SER - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - CYS Joining CYS - TYR Joining TYR - LYS Joining LYS - SER Joining SER - GLY Joining GLY - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - GLU Joining GLU - GLN Joining GLN - PHE Joining PHE - ILE Joining ILE - SER Joining SER - ALA Joining ALA - SER Joining SER - LYS Joining LYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - HIE Joining HIE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ASN Joining ASN - SER Joining SER - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - MET Joining MET - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASN Joining ASN - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ILE Joining ILE - SER Joining SER - LEU Joining LEU - PRO Joining PRO - THR Joining THR - SER Joining SER - CYS Joining CYS - ALA Joining ALA - SER Joining SER - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLN Joining GLN - CYS Joining CYS - LEU Joining LEU - ILE Joining ILE - SER Joining SER - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LYS Joining LYS - SER Joining SER - SER Joining SER - GLY Joining GLY - THR Joining THR - SER Joining SER - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - SER Joining SER - SER Joining SER - CYS Joining CYS - LYS Joining LYS - SER Joining SER - ALA Joining ALA - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - GLN Joining GLN - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - MET Joining MET - PHE Joining PHE - CYS Joining CYS - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - ASP Joining ASP - SER Joining SER - CYS Joining CYS - GLN Joining GLN - GLY Joining GLY - ASP Joining ASP - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - CYS Joining CYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - SER Joining SER - TRP Joining TRP - GLY Joining GLY - SER Joining SER - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLN Joining GLN - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - TYR Joining TYR - THR Joining THR - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - TRP Joining TRP - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - THR Joining THR - ILE Joining ILE - ALA Joining ALA - SER Joining SER - ASN Joining ASN - NME total atoms in file: 3263 > savemol2 test2 c2k_bzim_correct_xleap.mol2 1 saveMol2: Argument #1 is type String must be of type: [unit] usage: saveMol2