log started: Fri May 29 14:59:14 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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 gaff.dat Loading parameters: /opt/amber9/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > prot = loadpdb 2_dock_1YHL_A10CN_ris.pdb Loading PDB file: ./2_dock_1YHL_A10CN_ris.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: SER, Nonterminal, was not found in name map.) (Residue 3: MET, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: ARG, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: LEU, Nonterminal, was not found in name map.) (Residue 8: SER, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: TYR, Nonterminal, was not found in name map.) (Residue 11: ASP, Nonterminal, was not found in name map.) (Residue 12: GLU, Nonterminal, was not found in name map.) (Residue 13: VAL, Nonterminal, was not found in name map.) (Residue 14: GLN, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: PHE, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: GLN, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: GLN, Nonterminal, was not found in name map.) (Residue 23: SER, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: GLU, Nonterminal, was not found in name map.) (Residue 27: ILE, Nonterminal, was not found in name map.) (Residue 28: ASP, Nonterminal, was not found in name map.) (Residue 29: PRO, Nonterminal, was not found in name map.) (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: ALA, Nonterminal, was not found in name map.) (Residue 33: ARG, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: LEU, Nonterminal, was not found in name map.) (Residue 36: ARG, Nonterminal, was not found in name map.) (Residue 37: ILE, Nonterminal, was not found in name map.) (Residue 38: MET, Nonterminal, was not found in name map.) (Residue 39: MET, Nonterminal, was not found in name map.) (Residue 40: ASP, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: CYS, Nonterminal, was not found in name map.) (Residue 44: LEU, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: LYS, Nonterminal, was not found in name map.) (Residue 48: TYR, Nonterminal, was not found in name map.) (Residue 49: PHE, Nonterminal, was not found in name map.) (Residue 50: ARG, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: MET, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: VAL, Nonterminal, was not found in name map.) (Residue 55: VAL, 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: ALA, 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: PHE, Nonterminal, was not found in name map.) (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: ALA, Nonterminal, was not found in name map.) (Residue 64: VAL, Nonterminal, was not found in name map.) (Residue 65: THR, Nonterminal, was not found in name map.) (Residue 66: GLN, Nonterminal, was not found in name map.) (Residue 67: HIS, Nonterminal, was not found in name map.) (Residue 68: ASP, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: ALA, Nonterminal, was not found in name map.) (Residue 71: THR, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: GLU, Nonterminal, was not found in name map.) (Residue 74: ARG, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: HIS, Nonterminal, was not found in name map.) (Residue 78: ASP, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: CYS, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: GLY, Nonterminal, was not found in name map.) (Residue 84: TRP, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: GLU, Nonterminal, was not found in name map.) (Residue 88: PHE, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: GLN, Nonterminal, was not found in name map.) (Residue 91: ALA, Nonterminal, was not found in name map.) (Residue 92: HIS, Nonterminal, was not found in name map.) Mapped residue TYR, term: Terminal/last, seq. number: 93 to: CTYR. Mapped residue LEU, term: Terminal/beginning, seq. number: 94 to: NLEU. (Residue 95: VAL, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 97 to: CASP. Mapped residue ASP, term: Terminal/beginning, seq. number: 98 to: NASP. (Residue 99: ILE, Nonterminal, was not found in name map.) (Residue 100: MET, Nonterminal, was not found in name map.) (Residue 101: ASP, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: VAL, Nonterminal, was not found in name map.) (Residue 105: MET, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ARG, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: LYS, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: CYS, Nonterminal, was not found in name map.) (Residue 112: TRP, Nonterminal, was not found in name map.) (Residue 113: TYR, Nonterminal, was not found in name map.) (Residue 114: ARG, Nonterminal, was not found in name map.) (Residue 115: PHE, Nonterminal, was not found in name map.) (Residue 116: PRO, Nonterminal, was not found in name map.) (Residue 117: GLY, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: THR, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLN, Nonterminal, was not found in name map.) (Residue 122: CYS, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ILE, Nonterminal, was not found in name map.) (Residue 125: ASN, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: GLY, Nonterminal, was not found in name map.) (Residue 128: ILE, Nonterminal, was not found in name map.) (Residue 129: ILE, Nonterminal, was not found in name map.) (Residue 130: LEU, Nonterminal, was not found in name map.) (Residue 131: LYS, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: TRP, Nonterminal, was not found in name map.) (Residue 134: THR, Nonterminal, was not found in name map.) (Residue 135: GLN, Nonterminal, was not found in name map.) (Residue 136: ILE, Nonterminal, was not found in name map.) (Residue 137: MET, Nonterminal, was not found in name map.) (Residue 138: ALA, Nonterminal, was not found in name map.) (Residue 139: TRP, Nonterminal, was not found in name map.) (Residue 140: HIS, Nonterminal, was not found in name map.) (Residue 141: TYR, Nonterminal, was not found in name map.) (Residue 142: PHE, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: ASP, Nonterminal, was not found in name map.) (Residue 145: ARG, Nonterminal, was not found in name map.) (Residue 146: PRO, Nonterminal, was not found in name map.) (Residue 147: PHE, Nonterminal, was not found in name map.) (Residue 148: LEU, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: ASP, Nonterminal, was not found in name map.) (Residue 151: LEU, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: CYS, Nonterminal, was not found in name map.) (Residue 154: LEU, Nonterminal, was not found in name map.) (Residue 155: PHE, Nonterminal, was not found in name map.) (Residue 156: GLN, Nonterminal, was not found in name map.) (Residue 157: LYS, Nonterminal, was not found in name map.) (Residue 158: VAL, Nonterminal, was not found in name map.) (Residue 159: ASP, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: THR, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: VAL, Nonterminal, was not found in name map.) (Residue 165: GLY, Nonterminal, was not found in name map.) (Residue 166: GLN, Nonterminal, was not found in name map.) (Residue 167: MET, Nonterminal, was not found in name map.) (Residue 168: TYR, Nonterminal, was not found in name map.) (Residue 169: ASP, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: THR, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: MET, Nonterminal, was not found in name map.) (Residue 174: CYS, 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: ASN, Nonterminal, was not found in name map.) (Residue 178: LYS, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: ASP, Nonterminal, was not found in name map.) (Residue 181: PRO, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: VAL, Nonterminal, was not found in name map.) (Residue 184: ALA, Nonterminal, was not found in name map.) (Residue 185: GLN, Nonterminal, was not found in name map.) (Residue 186: PRO, Nonterminal, was not found in name map.) (Residue 187: MET, Nonterminal, was not found in name map.) (Residue 188: THR, Nonterminal, was not found in name map.) (Residue 189: THR, Nonterminal, was not found in name map.) (Residue 190: ASP, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: GLU, Nonterminal, was not found in name map.) (Residue 194: PHE, Nonterminal, was not found in name map.) (Residue 195: THR, Nonterminal, was not found in name map.) (Residue 196: PRO, Nonterminal, was not found in name map.) (Residue 197: ALA, Nonterminal, was not found in name map.) (Residue 198: ILE, Nonterminal, was not found in name map.) (Residue 199: TYR, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ARG, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: VAL, Nonterminal, was not found in name map.) (Residue 204: LYS, Nonterminal, was not found in name map.) (Residue 205: TYR, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 206 to: CLYS. Mapped residue THR, term: Terminal/beginning, seq. number: 207 to: NTHR. (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: TYR, Nonterminal, was not found in name map.) (Residue 211: THR, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: PRO, Nonterminal, was not found in name map.) (Residue 216: LEU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: MET, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: VAL, Nonterminal, was not found in name map.) (Residue 223: SER, Nonterminal, was not found in name map.) (Residue 224: GLU, Nonterminal, was not found in name map.) (Residue 225: ALA, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: ALA, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: VAL, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: MET, Nonterminal, was not found in name map.) (Residue 232: ASN, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: ARG, Nonterminal, was not found in name map.) (Residue 237: VAL, Nonterminal, was not found in name map.) (Residue 238: ALA, Nonterminal, was not found in name map.) (Residue 239: HIS, Nonterminal, was not found in name map.) (Residue 240: LEU, Nonterminal, was not found in name map.) (Residue 241: ILE, Nonterminal, was not found in name map.) (Residue 242: GLY, Nonterminal, was not found in name map.) (Residue 243: GLU, Nonterminal, was not found in name map.) (Residue 244: TYR, Nonterminal, was not found in name map.) (Residue 245: PHE, Nonterminal, was not found in name map.) (Residue 246: GLN, Nonterminal, was not found in name map.) (Residue 247: VAL, Nonterminal, was not found in name map.) (Residue 248: GLN, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 249 to: CASP. Mapped residue ASP, term: Terminal/beginning, seq. number: 250 to: NASP. (Residue 251: VAL, Nonterminal, was not found in name map.) (Residue 252: MET, Nonterminal, was not found in name map.) (Residue 253: ASP, Nonterminal, was not found in name map.) (Residue 254: CYS, Nonterminal, was not found in name map.) (Residue 255: PHE, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: PRO, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: GLN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: GLY, Nonterminal, was not found in name map.) (Residue 263: LYS, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: GLY, Nonterminal, was not found in name map.) (Residue 266: THR, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: ILE, Nonterminal, was not found in name map.) (Residue 269: GLU, Nonterminal, was not found in name map.) (Residue 270: ASP, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: LYS, Nonterminal, was not found in name map.) (Residue 273: CYS, Nonterminal, was not found in name map.) (Residue 274: SER, Nonterminal, was not found in name map.) (Residue 275: TRP, Nonterminal, was not found in name map.) (Residue 276: LEU, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: VAL, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: PHE, Nonterminal, was not found in name map.) (Residue 281: LEU, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: LYS, Nonterminal, was not found in name map.) (Residue 284: ALA, Nonterminal, was not found in name map.) (Residue 285: ASN, Nonterminal, was not found in name map.) (Residue 286: ALA, Nonterminal, was not found in name map.) (Residue 287: ALA, Nonterminal, was not found in name map.) (Residue 288: GLN, Nonterminal, was not found in name map.) (Residue 289: VAL, Nonterminal, was not found in name map.) (Residue 290: ALA, Nonterminal, was not found in name map.) (Residue 291: GLU, Nonterminal, was not found in name map.) (Residue 292: PHE, Nonterminal, was not found in name map.) (Residue 293: LYS, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: ASN, Nonterminal, was not found in name map.) (Residue 296: TYR, Nonterminal, was not found in name map.) (Residue 297: GLY, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: LYS, Nonterminal, was not found in name map.) (Residue 300: ASP, Nonterminal, was not found in name map.) (Residue 301: PRO, Nonterminal, was not found in name map.) (Residue 302: ALA, Nonterminal, was not found in name map.) (Residue 303: LYS, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ALA, Nonterminal, was not found in name map.) (Residue 306: VAL, Nonterminal, was not found in name map.) (Residue 307: VAL, Nonterminal, was not found in name map.) (Residue 308: LYS, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: LEU, Nonterminal, was not found in name map.) (Residue 311: TYR, Nonterminal, was not found in name map.) (Residue 312: SER, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: ALA, Nonterminal, was not found in name map.) (Residue 315: ASN, Nonterminal, was not found in name map.) (Residue 316: LEU, Nonterminal, was not found in name map.) (Residue 317: GLN, Nonterminal, was not found in name map.) (Residue 318: ALA, Nonterminal, was not found in name map.) (Residue 319: ASP, Nonterminal, was not found in name map.) (Residue 320: PHE, Nonterminal, was not found in name map.) (Residue 321: ALA, Nonterminal, was not found in name map.) (Residue 322: ALA, Nonterminal, was not found in name map.) (Residue 323: TYR, Nonterminal, was not found in name map.) (Residue 324: GLU, Nonterminal, was not found in name map.) (Residue 325: ALA, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: VAL, Nonterminal, was not found in name map.) (Residue 328: VAL, Nonterminal, was not found in name map.) (Residue 329: ARG, Nonterminal, was not found in name map.) (Residue 330: GLU, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: GLU, Nonterminal, was not found in name map.) (Residue 333: SER, Nonterminal, was not found in name map.) (Residue 334: LEU, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: GLU, Nonterminal, was not found in name map.) (Residue 337: GLN, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: LYS, Nonterminal, was not found in name map.) (Residue 340: VAL, Nonterminal, was not found in name map.) (Residue 341: LYS, Nonterminal, was not found in name map.) (Residue 342: SER, Nonterminal, was not found in name map.) (Residue 343: PRO, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: PHE, Nonterminal, was not found in name map.) (Residue 346: ALA, Nonterminal, was not found in name map.) (Residue 347: GLU, Nonterminal, was not found in name map.) (Residue 348: SER, Nonterminal, was not found in name map.) (Residue 349: VAL, Nonterminal, was not found in name map.) (Residue 350: ALA, Nonterminal, was not found in name map.) (Residue 351: VAL, Nonterminal, was not found in name map.) (Residue 352: VAL, Nonterminal, was not found in name map.) (Residue 353: TRP, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: LYS, Nonterminal, was not found in name map.) (Residue 356: THR, Nonterminal, was not found in name map.) (Residue 357: HIS, Nonterminal, was not found in name map.) (Residue 358: LYS, Nonterminal, was not found in name map.) (Residue 359: ARG, Nonterminal, was not found in name map.) (Residue 360: LYS, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 361 to: CLYS. (Residue 362: A0N, Terminal/beginning, was not found in name map.) Unknown residue: A0N number: 362 type: Terminal/beginning ..relaxing end constraints to try for a dbase match -no luck (Residue 363: DMA, Nonterminal, was not found in name map.) Unknown residue: DMA number: 363 type: Nonterminal (Residue 364: MG, Nonterminal, was not found in name map.) Unknown residue: MG number: 364 type: Nonterminal (Residue 365: MG, Nonterminal, was not found in name map.) Unknown residue: MG number: 365 type: Nonterminal (Residue 366: MG, Nonterminal, was not found in name map.) Unknown residue: MG number: 366 type: Nonterminal (Residue 367: SO4, Nonterminal, was not found in name map.) Unknown residue: SO4 number: 367 type: Nonterminal (Residue 368: HOH, Nonterminal, was not found in name map.) (Residue 369: HOH, Nonterminal, was not found in name map.) (Residue 370: HOH, Nonterminal, was not found in name map.) (Residue 371: HOH, Nonterminal, was not found in name map.) (Residue 372: HOH, Nonterminal, was not found in name map.) (Residue 373: HOH, Nonterminal, was not found in name map.) (Residue 374: HOH, Nonterminal, was not found in name map.) (Residue 375: HOH, Nonterminal, was not found in name map.) (Residue 376: HOH, Nonterminal, was not found in name map.) (Residue 377: HOH, Nonterminal, was not found in name map.) (Residue 378: HOH, Nonterminal, was not found in name map.) (Residue 379: HOH, Nonterminal, was not found in name map.) (Residue 380: HOH, Nonterminal, was not found in name map.) (Residue 381: HOH, Nonterminal, was not found in name map.) (Residue 382: HOH, Nonterminal, was not found in name map.) (Residue 383: HOH, Nonterminal, was not found in name map.) (Residue 384: HOH, Nonterminal, was not found in name map.) (Residue 385: HOH, Nonterminal, was not found in name map.) (Residue 386: HOH, Nonterminal, was not found in name map.) (Residue 387: HOH, Nonterminal, was not found in name map.) (Residue 388: HOH, Nonterminal, was not found in name map.) (Residue 389: HOH, Nonterminal, was not found in name map.) (Residue 390: HOH, Nonterminal, was not found in name map.) (Residue 391: HOH, Nonterminal, was not found in name map.) (Residue 392: HOH, Nonterminal, was not found in name map.) (Residue 393: HOH, Nonterminal, was not found in name map.) (Residue 394: HOH, Nonterminal, was not found in name map.) (Residue 395: HOH, Nonterminal, was not found in name map.) (Residue 396: HOH, Nonterminal, was not found in name map.) (Residue 397: HOH, Nonterminal, was not found in name map.) (Residue 398: HOH, Nonterminal, was not found in name map.) (Residue 399: HOH, Nonterminal, was not found in name map.) (Residue 400: HOH, Nonterminal, was not found in name map.) (Residue 401: HOH, Nonterminal, was not found in name map.) (Residue 402: HOH, Nonterminal, was not found in name map.) (Residue 403: HOH, Nonterminal, was not found in name map.) (Residue 404: HOH, Nonterminal, was not found in name map.) (Residue 405: HOH, Nonterminal, was not found in name map.) (Residue 406: HOH, Nonterminal, was not found in name map.) (Residue 407: HOH, Nonterminal, was not found in name map.) (Residue 408: HOH, Nonterminal, was not found in name map.) (Residue 409: HOH, Nonterminal, was not found in name map.) (Residue 410: HOH, Nonterminal, was not found in name map.) (Residue 411: HOH, Nonterminal, was not found in name map.) (Residue 412: HOH, Nonterminal, was not found in name map.) (Residue 413: HOH, Nonterminal, was not found in name map.) (Residue 414: HOH, Nonterminal, was not found in name map.) (Residue 415: HOH, Nonterminal, was not found in name map.) (Residue 416: HOH, Nonterminal, was not found in name map.) (Residue 417: HOH, Nonterminal, was not found in name map.) (Residue 418: HOH, Nonterminal, was not found in name map.) (Residue 419: HOH, Nonterminal, was not found in name map.) (Residue 420: HOH, Nonterminal, was not found in name map.) (Residue 421: HOH, Nonterminal, was not found in name map.) (Residue 422: HOH, Nonterminal, was not found in name map.) (Residue 423: HOH, Nonterminal, was not found in name map.) (Residue 424: HOH, Nonterminal, was not found in name map.) (Residue 425: HOH, Nonterminal, was not found in name map.) (Residue 426: HOH, Nonterminal, was not found in name map.) (Residue 427: HOH, Nonterminal, was not found in name map.) (Residue 428: HOH, Nonterminal, was not found in name map.) (Residue 429: HOH, Nonterminal, was not found in name map.) (Residue 430: HOH, Nonterminal, was not found in name map.) (Residue 431: HOH, Nonterminal, was not found in name map.) (Residue 432: HOH, Nonterminal, was not found in name map.) (Residue 433: HOH, Nonterminal, was not found in name map.) (Residue 434: HOH, Nonterminal, was not found in name map.) (Residue 435: HOH, Nonterminal, was not found in name map.) (Residue 436: HOH, Nonterminal, was not found in name map.) (Residue 437: HOH, Nonterminal, was not found in name map.) (Residue 438: HOH, Nonterminal, was not found in name map.) (Residue 439: HOH, Nonterminal, was not found in name map.) (Residue 440: HOH, Nonterminal, was not found in name map.) (Residue 441: HOH, Nonterminal, was not found in name map.) (Residue 442: HOH, Nonterminal, was not found in name map.) (Residue 443: HOH, Nonterminal, was not found in name map.) (Residue 444: HOH, Nonterminal, was not found in name map.) (Residue 445: HOH, Nonterminal, was not found in name map.) (Residue 446: HOH, Nonterminal, was not found in name map.) (Residue 447: HOH, Nonterminal, was not found in name map.) (Residue 448: HOH, Nonterminal, was not found in name map.) (Residue 449: HOH, Nonterminal, was not found in name map.) (Residue 450: HOH, Nonterminal, was not found in name map.) (Residue 451: HOH, Nonterminal, was not found in name map.) (Residue 452: HOH, Nonterminal, was not found in name map.) (Residue 453: HOH, Nonterminal, was not found in name map.) (Residue 454: HOH, Nonterminal, was not found in name map.) (Residue 455: HOH, Nonterminal, was not found in name map.) (Residue 456: HOH, Nonterminal, was not found in name map.) (Residue 457: HOH, Nonterminal, was not found in name map.) (Residue 458: HOH, Nonterminal, was not found in name map.) (Residue 459: HOH, Nonterminal, was not found in name map.) (Residue 460: HOH, Nonterminal, was not found in name map.) (Residue 461: HOH, Nonterminal, was not found in name map.) (Residue 462: HOH, Nonterminal, was not found in name map.) (Residue 463: HOH, Nonterminal, was not found in name map.) (Residue 464: HOH, Nonterminal, was not found in name map.) (Residue 465: HOH, Nonterminal, was not found in name map.) (Residue 466: HOH, Nonterminal, was not found in name map.) (Residue 467: HOH, Nonterminal, was not found in name map.) (Residue 468: HOH, Nonterminal, was not found in name map.) (Residue 469: HOH, Nonterminal, was not found in name map.) (Residue 470: HOH, Nonterminal, was not found in name map.) (Residue 471: HOH, Nonterminal, was not found in name map.) (Residue 472: HOH, Nonterminal, was not found in name map.) (Residue 473: HOH, Nonterminal, was not found in name map.) (Residue 474: HOH, Nonterminal, was not found in name map.) (Residue 475: HOH, Nonterminal, was not found in name map.) (Residue 476: HOH, Nonterminal, was not found in name map.) (Residue 477: HOH, Nonterminal, was not found in name map.) (Residue 478: HOH, Nonterminal, was not found in name map.) (Residue 479: HOH, Nonterminal, was not found in name map.) (Residue 480: HOH, Nonterminal, was not found in name map.) (Residue 481: HOH, Nonterminal, was not found in name map.) (Residue 482: HOH, Nonterminal, was not found in name map.) (Residue 483: HOH, Nonterminal, was not found in name map.) (Residue 484: HOH, Nonterminal, was not found in name map.) (Residue 485: HOH, Nonterminal, was not found in name map.) (Residue 486: HOH, Nonterminal, was not found in name map.) (Residue 487: HOH, Nonterminal, was not found in name map.) (Residue 488: HOH, Nonterminal, was not found in name map.) (Residue 489: HOH, Nonterminal, was not found in name map.) (Residue 490: HOH, Nonterminal, was not found in name map.) (Residue 491: HOH, Nonterminal, was not found in name map.) (Residue 492: HOH, Nonterminal, was not found in name map.) (Residue 493: HOH, Nonterminal, was not found in name map.) (Residue 494: HOH, Nonterminal, was not found in name map.) (Residue 495: HOH, Nonterminal, was not found in name map.) (Residue 496: HOH, Nonterminal, was not found in name map.) (Residue 497: HOH, Nonterminal, was not found in name map.) (Residue 498: HOH, Nonterminal, was not found in name map.) (Residue 499: HOH, Nonterminal, was not found in name map.) (Residue 500: HOH, Nonterminal, was not found in name map.) (Residue 501: HOH, Nonterminal, was not found in name map.) (Residue 502: HOH, Nonterminal, was not found in name map.) (Residue 503: HOH, Nonterminal, was not found in name map.) (Residue 504: HOH, Nonterminal, was not found in name map.) (Residue 505: HOH, Nonterminal, was not found in name map.) (Residue 506: HOH, Nonterminal, was not found in name map.) (Residue 507: HOH, Nonterminal, was not found in name map.) (Residue 508: HOH, Nonterminal, was not found in name map.) (Residue 509: HOH, Nonterminal, was not found in name map.) (Residue 510: HOH, Nonterminal, was not found in name map.) (Residue 511: HOH, Nonterminal, was not found in name map.) (Residue 512: HOH, Nonterminal, was not found in name map.) (Residue 513: HOH, Nonterminal, was not found in name map.) (Residue 514: HOH, Nonterminal, was not found in name map.) (Residue 515: HOH, Nonterminal, was not found in name map.) (Residue 516: HOH, Nonterminal, was not found in name map.) (Residue 517: HOH, Nonterminal, was not found in name map.) (Residue 518: HOH, Nonterminal, was not found in name map.) (Residue 519: HOH, Nonterminal, was not found in name map.) (Residue 520: HOH, Nonterminal, was not found in name map.) (Residue 521: HOH, Nonterminal, was not found in name map.) (Residue 522: HOH, Nonterminal, was not found in name map.) (Residue 523: HOH, Nonterminal, was not found in name map.) (Residue 524: HOH, Nonterminal, was not found in name map.) (Residue 525: HOH, Nonterminal, was not found in name map.) (Residue 526: HOH, Nonterminal, was not found in name map.) (Residue 527: HOH, Nonterminal, was not found in name map.) (Residue 528: HOH, Nonterminal, was not found in name map.) (Residue 529: HOH, Nonterminal, was not found in name map.) (Residue 530: HOH, Nonterminal, was not found in name map.) (Residue 531: HOH, Nonterminal, was not found in name map.) (Residue 532: HOH, Nonterminal, was not found in name map.) (Residue 533: HOH, Nonterminal, was not found in name map.) (Residue 534: HOH, Nonterminal, was not found in name map.) (Residue 535: HOH, Nonterminal, was not found in name map.) (Residue 536: HOH, Nonterminal, was not found in name map.) (Residue 537: HOH, Nonterminal, was not found in name map.) (Residue 538: HOH, Nonterminal, was not found in name map.) (Residue 539: HOH, Nonterminal, was not found in name map.) (Residue 540: HOH, Nonterminal, was not found in name map.) (Residue 541: HOH, Nonterminal, was not found in name map.) (Residue 542: HOH, Nonterminal, was not found in name map.) (Residue 543: HOH, Nonterminal, was not found in name map.) (Residue 544: HOH, Nonterminal, was not found in name map.) (Residue 545: HOH, Nonterminal, was not found in name map.) (Residue 546: HOH, Nonterminal, was not found in name map.) (Residue 547: HOH, Nonterminal, was not found in name map.) (Residue 548: HOH, Nonterminal, was not found in name map.) (Residue 549: HOH, Nonterminal, was not found in name map.) (Residue 550: HOH, Nonterminal, was not found in name map.) (Residue 551: HOH, Nonterminal, was not found in name map.) (Residue 552: HOH, Nonterminal, was not found in name map.) (Residue 553: HOH, Nonterminal, was not found in name map.) (Residue 554: HOH, Nonterminal, was not found in name map.) (Residue 555: HOH, Nonterminal, was not found in name map.) (Residue 556: HOH, Nonterminal, was not found in name map.) (Residue 557: HOH, Nonterminal, was not found in name map.) (Residue 558: HOH, Nonterminal, was not found in name map.) (Residue 559: HOH, Nonterminal, was not found in name map.) (Residue 560: HOH, Nonterminal, was not found in name map.) (Residue 561: HOH, Nonterminal, was not found in name map.) (Residue 562: HOH, Nonterminal, was not found in name map.) (Residue 563: HOH, Nonterminal, was not found in name map.) (Residue 564: HOH, Nonterminal, was not found in name map.) (Residue 565: HOH, Nonterminal, was not found in name map.) (Residue 566: HOH, Nonterminal, was not found in name map.) (Residue 567: HOH, Nonterminal, was not found in name map.) (Residue 568: HOH, Nonterminal, was not found in name map.) (Residue 569: HOH, Nonterminal, was not found in name map.) (Residue 570: HOH, Nonterminal, was not found in name map.) (Residue 571: HOH, Nonterminal, was not found in name map.) (Residue 572: HOH, Nonterminal, was not found in name map.) (Residue 573: HOH, Nonterminal, was not found in name map.) (Residue 574: HOH, Nonterminal, was not found in name map.) (Residue 575: HOH, Nonterminal, was not found in name map.) (Residue 576: HOH, Nonterminal, was not found in name map.) (Residue 577: HOH, Nonterminal, was not found in name map.) (Residue 578: HOH, Nonterminal, was not found in name map.) (Residue 579: HOH, Nonterminal, was not found in name map.) (Residue 580: HOH, Nonterminal, was not found in name map.) (Residue 581: HOH, Nonterminal, was not found in name map.) (Residue 582: HOH, Nonterminal, was not found in name map.) (Residue 583: HOH, Nonterminal, was not found in name map.) (Residue 584: HOH, Nonterminal, was not found in name map.) (Residue 585: HOH, Nonterminal, was not found in name map.) (Residue 586: HOH, Nonterminal, was not found in name map.) (Residue 587: HOH, Nonterminal, was not found in name map.) (Residue 588: HOH, Nonterminal, was not found in name map.) (Residue 589: HOH, Nonterminal, was not found in name map.) (Residue 590: HOH, Nonterminal, was not found in name map.) (Residue 591: HOH, Nonterminal, was not found in name map.) (Residue 592: HOH, Nonterminal, was not found in name map.) (Residue 593: HOH, Nonterminal, was not found in name map.) (Residue 594: HOH, Nonterminal, was not found in name map.) (Residue 595: HOH, Nonterminal, was not found in name map.) (Residue 596: HOH, Nonterminal, was not found in name map.) (Residue 597: HOH, Nonterminal, was not found in name map.) (Residue 598: HOH, Nonterminal, was not found in name map.) (Residue 599: HOH, Nonterminal, was not found in name map.) (Residue 600: HOH, Nonterminal, was not found in name map.) (Residue 601: HOH, Nonterminal, was not found in name map.) (Residue 602: HOH, Nonterminal, was not found in name map.) (Residue 603: HOH, Nonterminal, was not found in name map.) (Residue 604: HOH, Nonterminal, was not found in name map.) (Residue 605: HOH, Nonterminal, was not found in name map.) (Residue 606: HOH, Nonterminal, was not found in name map.) (Residue 607: HOH, Nonterminal, was not found in name map.) (Residue 608: HOH, Nonterminal, was not found in name map.) (Residue 609: HOH, Nonterminal, was not found in name map.) (Residue 610: HOH, Nonterminal, was not found in name map.) (Residue 611: HOH, Nonterminal, was not found in name map.) (Residue 612: HOH, Nonterminal, was not found in name map.) (Residue 613: HOH, Nonterminal, was not found in name map.) (Residue 614: HOH, Nonterminal, was not found in name map.) (Residue 615: HOH, Nonterminal, was not found in name map.) (Residue 616: HOH, Nonterminal, was not found in name map.) (Residue 617: HOH, Nonterminal, was not found in name map.) (Residue 618: HOH, Nonterminal, was not found in name map.) (Residue 619: HOH, Nonterminal, was not found in name map.) (Residue 620: HOH, Nonterminal, was not found in name map.) (Residue 621: HOH, Nonterminal, was not found in name map.) (Residue 622: HOH, Nonterminal, was not found in name map.) (Residue 623: HOH, Nonterminal, was not found in name map.) (Residue 624: HOH, Nonterminal, was not found in name map.) (Residue 625: HOH, Nonterminal, was not found in name map.) (Residue 626: HOH, Nonterminal, was not found in name map.) (Residue 627: HOH, Nonterminal, was not found in name map.) (Residue 628: HOH, Nonterminal, was not found in name map.) (Residue 629: HOH, Nonterminal, was not found in name map.) (Residue 630: HOH, Nonterminal, was not found in name map.) (Residue 631: HOH, Nonterminal, was not found in name map.) (Residue 632: HOH, Nonterminal, was not found in name map.) (Residue 633: HOH, Nonterminal, was not found in name map.) (Residue 634: HOH, Nonterminal, was not found in name map.) (Residue 635: HOH, Nonterminal, was not found in name map.) (Residue 636: HOH, Nonterminal, was not found in name map.) (Residue 637: HOH, Nonterminal, was not found in name map.) (Residue 638: HOH, Nonterminal, was not found in name map.) (Residue 639: HOH, Nonterminal, was not found in name map.) (Residue 640: HOH, Nonterminal, was not found in name map.) (Residue 641: HOH, Nonterminal, was not found in name map.) (Residue 642: HOH, Nonterminal, was not found in name map.) (Residue 643: HOH, Nonterminal, was not found in name map.) (Residue 644: HOH, Nonterminal, was not found in name map.) (Residue 645: HOH, Nonterminal, was not found in name map.) (Residue 646: HOH, Nonterminal, was not found in name map.) (Residue 647: HOH, Nonterminal, was not found in name map.) (Residue 648: HOH, Nonterminal, was not found in name map.) (Residue 649: HOH, Nonterminal, was not found in name map.) (Residue 650: HOH, Nonterminal, was not found in name map.) (Residue 651: HOH, Nonterminal, was not found in name map.) (Residue 652: HOH, Nonterminal, was not found in name map.) (Residue 653: HOH, Nonterminal, was not found in name map.) (Residue 654: HOH, Nonterminal, was not found in name map.) (Residue 655: HOH, Nonterminal, was not found in name map.) (Residue 656: HOH, Nonterminal, was not found in name map.) (Residue 657: HOH, Nonterminal, was not found in name map.) (Residue 658: HOH, Nonterminal, was not found in name map.) (Residue 659: HOH, Nonterminal, was not found in name map.) (Residue 660: HOH, Nonterminal, was not found in name map.) (Residue 661: HOH, Nonterminal, was not found in name map.) (Residue 662: HOH, Nonterminal, was not found in name map.) (Residue 663: HOH, Nonterminal, was not found in name map.) (Residue 664: HOH, Nonterminal, was not found in name map.) (Residue 665: HOH, Nonterminal, was not found in name map.) (Residue 666: HOH, Nonterminal, was not found in name map.) (Residue 667: HOH, Nonterminal, was not found in name map.) (Residue 668: HOH, Nonterminal, was not found in name map.) (Residue 669: HOH, Nonterminal, was not found in name map.) (Residue 670: HOH, Nonterminal, was not found in name map.) (Residue 671: HOH, Nonterminal, was not found in name map.) (Residue 672: HOH, Nonterminal, was not found in name map.) (Residue 673: HOH, Nonterminal, was not found in name map.) (Residue 674: HOH, Nonterminal, was not found in name map.) (Residue 675: HOH, Nonterminal, was not found in name map.) (Residue 676: HOH, Nonterminal, was not found in name map.) (Residue 677: HOH, Nonterminal, was not found in name map.) (Residue 678: HOH, Nonterminal, was not found in name map.) (Residue 679: HOH, Nonterminal, was not found in name map.) (Residue 680: HOH, Nonterminal, was not found in name map.) (Residue 681: HOH, Nonterminal, was not found in name map.) (Residue 682: HOH, Nonterminal, was not found in name map.) (Residue 683: HOH, Nonterminal, was not found in name map.) (Residue 684: HOH, Nonterminal, was not found in name map.) (Residue 685: HOH, Nonterminal, was not found in name map.) (Residue 686: HOH, Nonterminal, was not found in name map.) (Residue 687: HOH, Nonterminal, was not found in name map.) (Residue 688: HOH, Nonterminal, was not found in name map.) (Residue 689: HOH, Nonterminal, was not found in name map.) (Residue 690: HOH, Nonterminal, was not found in name map.) (Residue 691: HOH, Nonterminal, was not found in name map.) (Residue 692: HOH, Nonterminal, was not found in name map.) (Residue 693: HOH, Nonterminal, was not found in name map.) (Residue 694: HOH, Nonterminal, was not found in name map.) (Residue 695: HOH, Nonterminal, was not found in name map.) (Residue 696: HOH, Nonterminal, was not found in name map.) (Residue 697: HOH, Nonterminal, was not found in name map.) (Residue 698: HOH, Nonterminal, was not found in name map.) (Residue 699: HOH, Nonterminal, was not found in name map.) (Residue 700: HOH, Nonterminal, was not found in name map.) (Residue 701: HOH, Nonterminal, was not found in name map.) (Residue 702: HOH, Nonterminal, was not found in name map.) (Residue 703: HOH, Nonterminal, was not found in name map.) (Residue 704: HOH, Nonterminal, was not found in name map.) (Residue 705: HOH, Nonterminal, was not found in name map.) (Residue 706: HOH, Nonterminal, was not found in name map.) (Residue 707: HOH, Nonterminal, was not found in name map.) (Residue 708: HOH, Nonterminal, was not found in name map.) (Residue 709: HOH, Nonterminal, was not found in name map.) (Residue 710: HOH, Nonterminal, was not found in name map.) (Residue 711: HOH, Nonterminal, was not found in name map.) (Residue 712: HOH, Nonterminal, was not found in name map.) (Residue 713: HOH, Nonterminal, was not found in name map.) (Residue 714: HOH, Nonterminal, was not found in name map.) (Residue 715: HOH, Nonterminal, was not found in name map.) (Residue 716: HOH, Nonterminal, was not found in name map.) (Residue 717: HOH, Nonterminal, was not found in name map.) (Residue 718: HOH, Nonterminal, was not found in name map.) (Residue 719: HOH, Nonterminal, was not found in name map.) (Residue 720: HOH, Nonterminal, was not found in name map.) (Residue 721: HOH, Nonterminal, was not found in name map.) (Residue 722: HOH, Nonterminal, was not found in name map.) (Residue 723: HOH, Nonterminal, was not found in name map.) (Residue 724: HOH, Nonterminal, was not found in name map.) (Residue 725: HOH, Nonterminal, was not found in name map.) (Residue 726: HOH, Nonterminal, was not found in name map.) (Residue 727: HOH, Nonterminal, was not found in name map.) (Residue 728: HOH, Nonterminal, was not found in name map.) (Residue 729: HOH, Nonterminal, was not found in name map.) (Residue 730: HOH, Nonterminal, was not found in name map.) (Residue 731: HOH, Nonterminal, was not found in name map.) (Residue 732: HOH, Nonterminal, was not found in name map.) (Residue 733: HOH, Nonterminal, was not found in name map.) (Residue 734: HOH, Nonterminal, was not found in name map.) (Residue 735: HOH, Nonterminal, was not found in name map.) (Residue 736: HOH, Nonterminal, was not found in name map.) (Residue 737: HOH, Nonterminal, was not found in name map.) (Residue 738: HOH, Nonterminal, was not found in name map.) (Residue 739: HOH, Nonterminal, was not found in name map.) (Residue 740: HOH, Nonterminal, was not found in name map.) (Residue 741: HOH, Nonterminal, was not found in name map.) (Residue 742: HOH, Nonterminal, was not found in name map.) (Residue 743: HOH, Nonterminal, was not found in name map.) (Residue 744: HOH, Nonterminal, was not found in name map.) (Residue 745: HOH, Nonterminal, was not found in name map.) (Residue 746: HOH, Nonterminal, was not found in name map.) (Residue 747: HOH, Nonterminal, was not found in name map.) (Residue 748: HOH, Nonterminal, was not found in name map.) (Residue 749: HOH, Nonterminal, was not found in name map.) (Residue 750: HOH, Nonterminal, was not found in name map.) (Residue 751: HOH, Nonterminal, was not found in name map.) (Residue 752: HOH, Nonterminal, was not found in name map.) (Residue 753: HOH, Nonterminal, was not found in name map.) (Residue 754: HOH, Nonterminal, was not found in name map.) (Residue 755: HOH, Nonterminal, was not found in name map.) (Residue 756: HOH, Nonterminal, was not found in name map.) (Residue 757: HOH, Nonterminal, was not found in name map.) (Residue 758: HOH, Nonterminal, was not found in name map.) (Residue 759: HOH, Terminal/last, was not found in name map.) Joining NMET - ALA Joining ALA - SER Joining SER - MET Joining MET - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - SER Joining SER - VAL Joining VAL - TYR Joining TYR - ASP Joining ASP - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - GLN Joining GLN - SER Joining SER - LYS Joining LYS - TYR Joining TYR - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - ASN Joining ASN - ARG Joining ARG - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - MET Joining MET - MET Joining MET - ASP Joining ASP - THR Joining THR - THR Joining THR - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - PHE Joining PHE - ARG Joining ARG - GLY Joining GLY - MET Joining MET - THR Joining THR - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - VAL Joining VAL - THR Joining THR - GLN Joining GLN - HIE Joining HIE - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - THR Joining THR - LYS Joining LYS - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - ALA Joining ALA - CYS Joining CYS - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TRP Joining TRP - MET Joining MET - ILE Joining ILE - GLU Joining GLU - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - CTYR Added missing heavy atom: .R.A Joining NLEU - VAL Joining VAL - GLU Joining GLU - CASP Added missing heavy atom: .R.A Joining NASP - ILE Joining ILE - MET Joining MET - ASP Joining ASP - GLY Joining GLY - SER Joining SER - VAL Joining VAL - MET Joining MET - ARG Joining ARG - ARG Joining ARG - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - TRP Joining TRP - TYR Joining TYR - ARG Joining ARG - PHE Joining PHE - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - THR Joining THR - THR Joining THR - GLN Joining GLN - CYS Joining CYS - ALA Joining ALA - ILE Joining ILE - ASN Joining ASN - ASP Joining ASP - GLY Joining GLY - ILE Joining ILE - ILE Joining ILE - LEU Joining LEU - LYS Joining LYS - SER Joining SER - TRP Joining TRP - THR Joining THR - GLN Joining GLN - ILE Joining ILE - MET Joining MET - ALA Joining ALA - TRP Joining TRP - HIE Joining HIE - TYR Joining TYR - PHE Joining PHE - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - LEU Joining LEU - LEU Joining LEU - CYS Joining CYS - LEU Joining LEU - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - VAL Joining VAL - ASP Joining ASP - TYR Joining TYR - ALA Joining ALA - THR Joining THR - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - GLN Joining GLN - MET Joining MET - TYR Joining TYR - ASP Joining ASP - VAL Joining VAL - THR Joining THR - SER Joining SER - MET Joining MET - CYS Joining CYS - ASP Joining ASP - SER Joining SER - ASN Joining ASN - LYS Joining LYS - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - MET Joining MET - THR Joining THR - THR Joining THR - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - GLU Joining GLU - PHE Joining PHE - THR Joining THR - PRO Joining PRO - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - LYS Joining LYS - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - LYS Joining LYS - TYR Joining TYR - CLYS Added missing heavy atom: .R.A Joining NTHR - THR Joining THR - PHE Joining PHE - TYR Joining TYR - THR Joining THR - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - VAL Joining VAL - MET Joining MET - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - VAL Joining VAL - SER Joining SER - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - GLU Joining GLU - MET Joining MET - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - HIE Joining HIE - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - GLU Joining GLU - TYR Joining TYR - PHE Joining PHE - GLN Joining GLN - VAL Joining VAL - GLN Joining GLN - CASP Added missing heavy atom: .R.A Joining NASP - VAL Joining VAL - MET Joining MET - ASP Joining ASP - CYS Joining CYS - PHE Joining PHE - THR Joining THR - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - GLN Joining GLN - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - THR Joining THR - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - ALA Joining ALA - LYS Joining LYS - CYS Joining CYS - SER Joining SER - TRP Joining TRP - LEU Joining LEU - ALA Joining ALA - VAL Joining VAL - THR Joining THR - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - PHE Joining PHE - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - TYR Joining TYR - SER Joining SER - GLU Joining GLU - ALA Joining ALA - ASN Joining ASN - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - ALA Joining ALA - TYR Joining TYR - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - LYS Joining LYS - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - ALA Joining ALA - GLU Joining GLU - SER Joining SER - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - THR Joining THR - HIE Joining HIE - LYS Joining LYS - ARG Joining ARG - LYS Joining LYS - CLYS Added missing heavy atom: .R.A Creating new UNIT for residue: A0N sequence: 363 Created a new atom named: CAG within residue: .R Created a new atom named: NAI within residue: .R Created a new atom named: CAK within residue: .R Created a new atom named: CAH within residue: .R Created a new atom named: CAF within residue: .R Created a new atom named: CAE within residue: .R Created a new atom named: CAL within residue: .R Created a new atom named: CAJ within residue: .R Created a new atom named: CAA within residue: .R Created a new atom named: CAD within residue: .R Created a new atom named: OAC within residue: .R Created a new atom named: NAB within residue: .R Created a new atom named: H004 within residue: .R Created a new atom named: H001 within residue: .R Created a new atom named: H002 within residue: .R Created a new atom named: H003 within residue: .R Created a new atom named: H005 within residue: .R Created a new atom named: H007 within residue: .R Created a new atom named: H006 within residue: .R Created a new atom named: HAA within residue: .R Creating new UNIT for residue: DMA sequence: 364 Starting new chain with Created a new atom named: C1 within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: PA within residue: .R Created a new atom named: O1A within residue: .R Created a new atom named: O2A within residue: .R Created a new atom named: O3A within residue: .R Created a new atom named: PB within residue: .R Created a new atom named: O1B within residue: .R Created a new atom named: O2B within residue: .R Created a new atom named: O3B within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: H12 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H41 within residue: .R Created a new atom named: H42 within residue: .R Created a new atom named: H43 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Created a new atom named: H1B within residue: .R Creating new UNIT for residue: MG sequence: 365 Starting new chain with Created a new atom named: MG within residue: .R Creating new UNIT for residue: MG sequence: 366 Starting new chain with Created a new atom named: MG within residue: .R Creating new UNIT for residue: MG sequence: 367 Starting new chain with Created a new atom named: MG within residue: .R Creating new UNIT for residue: SO4 sequence: 368 Starting new chain with Created a new atom named: S within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: O3 within residue: .R Created a new atom named: O4 within residue: .R Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 total atoms in file: 3335 Leap added 3653 missing atoms according to residue templates: 5 Heavy 3648 H / lone pairs The file contained 52 atoms not in residue templates > saveamberparm prot 1yhl_a0n.prmtop 1yhl_a0n.prmcrd Checking Unit. WARNING: The unperturbed charge of the unit: -11.000000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. > loadamberparams A0N.frcmod Loading parameters: ./A0N.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberprep A0N.prepc Could not open file A0N.prepc: not found > loadamberprep A0N_sybyl_gaff.prepc Loading Prep file: ./A0N_sybyl_gaff.prepc (UNKNOWN ATOM TYPE: n1) Loaded UNIT: A0N > saveamberparm prot 1yhl_a0n.prmtop 1yhl_a0n.prmcrd Checking Unit. WARNING: The unperturbed charge of the unit: -11.000000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. > list A0N 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 RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL WAT frcmod03 parm99 prot > edit A0N > desc A0N UNIT name: A0N Head atom: .R.A Tail atom: .R.A Contents: R > des A0N.1 ERROR: syntax error log started: Fri May 29 16:23:40 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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 > > list 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 RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL WAT frcmod03 parm99 > prot = loadpdb 2_dock_1YHL_A10CN_ris.pdb Loading PDB file: ./2_dock_1YHL_A10CN_ris.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: SER, Nonterminal, was not found in name map.) (Residue 3: MET, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: ARG, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: LEU, Nonterminal, was not found in name map.) (Residue 8: SER, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: TYR, Nonterminal, was not found in name map.) (Residue 11: ASP, Nonterminal, was not found in name map.) (Residue 12: GLU, Nonterminal, was not found in name map.) (Residue 13: VAL, Nonterminal, was not found in name map.) (Residue 14: GLN, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: PHE, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: LEU, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: GLN, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: GLN, Nonterminal, was not found in name map.) (Residue 23: SER, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: GLU, Nonterminal, was not found in name map.) (Residue 27: ILE, Nonterminal, was not found in name map.) (Residue 28: ASP, Nonterminal, was not found in name map.) (Residue 29: PRO, Nonterminal, was not found in name map.) (Residue 30: ASN, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: ALA, Nonterminal, was not found in name map.) (Residue 33: ARG, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: LEU, Nonterminal, was not found in name map.) (Residue 36: ARG, Nonterminal, was not found in name map.) (Residue 37: ILE, Nonterminal, was not found in name map.) (Residue 38: MET, Nonterminal, was not found in name map.) (Residue 39: MET, Nonterminal, was not found in name map.) (Residue 40: ASP, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: CYS, Nonterminal, was not found in name map.) (Residue 44: LEU, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: LYS, Nonterminal, was not found in name map.) (Residue 48: TYR, Nonterminal, was not found in name map.) (Residue 49: PHE, Nonterminal, was not found in name map.) (Residue 50: ARG, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: MET, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: VAL, Nonterminal, was not found in name map.) (Residue 55: VAL, 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: ALA, 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: PHE, Nonterminal, was not found in name map.) (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: ALA, Nonterminal, was not found in name map.) (Residue 64: VAL, Nonterminal, was not found in name map.) (Residue 65: THR, Nonterminal, was not found in name map.) (Residue 66: GLN, Nonterminal, was not found in name map.) (Residue 67: HIS, Nonterminal, was not found in name map.) (Residue 68: ASP, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: ALA, Nonterminal, was not found in name map.) (Residue 71: THR, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: GLU, Nonterminal, was not found in name map.) (Residue 74: ARG, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: HIS, Nonterminal, was not found in name map.) (Residue 78: ASP, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: CYS, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: GLY, Nonterminal, was not found in name map.) (Residue 84: TRP, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: GLU, Nonterminal, was not found in name map.) (Residue 88: PHE, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: GLN, Nonterminal, was not found in name map.) (Residue 91: ALA, Nonterminal, was not found in name map.) (Residue 92: HIS, Nonterminal, was not found in name map.) Mapped residue TYR, term: Terminal/last, seq. number: 93 to: CTYR. Mapped residue LEU, term: Terminal/beginning, seq. number: 94 to: NLEU. (Residue 95: VAL, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 97 to: CASP. Mapped residue ASP, term: Terminal/beginning, seq. number: 98 to: NASP. (Residue 99: ILE, Nonterminal, was not found in name map.) (Residue 100: MET, Nonterminal, was not found in name map.) (Residue 101: ASP, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: VAL, Nonterminal, was not found in name map.) (Residue 105: MET, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ARG, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: LYS, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: CYS, Nonterminal, was not found in name map.) (Residue 112: TRP, Nonterminal, was not found in name map.) (Residue 113: TYR, Nonterminal, was not found in name map.) (Residue 114: ARG, Nonterminal, was not found in name map.) (Residue 115: PHE, Nonterminal, was not found in name map.) (Residue 116: PRO, Nonterminal, was not found in name map.) (Residue 117: GLY, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: THR, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLN, Nonterminal, was not found in name map.) (Residue 122: CYS, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ILE, Nonterminal, was not found in name map.) (Residue 125: ASN, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: GLY, Nonterminal, was not found in name map.) (Residue 128: ILE, Nonterminal, was not found in name map.) (Residue 129: ILE, Nonterminal, was not found in name map.) (Residue 130: LEU, Nonterminal, was not found in name map.) (Residue 131: LYS, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: TRP, Nonterminal, was not found in name map.) (Residue 134: THR, Nonterminal, was not found in name map.) (Residue 135: GLN, Nonterminal, was not found in name map.) (Residue 136: ILE, Nonterminal, was not found in name map.) (Residue 137: MET, Nonterminal, was not found in name map.) (Residue 138: ALA, Nonterminal, was not found in name map.) (Residue 139: TRP, Nonterminal, was not found in name map.) (Residue 140: HIS, Nonterminal, was not found in name map.) (Residue 141: TYR, Nonterminal, was not found in name map.) (Residue 142: PHE, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: ASP, Nonterminal, was not found in name map.) (Residue 145: ARG, Nonterminal, was not found in name map.) (Residue 146: PRO, Nonterminal, was not found in name map.) (Residue 147: PHE, Nonterminal, was not found in name map.) (Residue 148: LEU, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: ASP, Nonterminal, was not found in name map.) (Residue 151: LEU, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: CYS, Nonterminal, was not found in name map.) (Residue 154: LEU, Nonterminal, was not found in name map.) (Residue 155: PHE, Nonterminal, was not found in name map.) (Residue 156: GLN, Nonterminal, was not found in name map.) (Residue 157: LYS, Nonterminal, was not found in name map.) (Residue 158: VAL, Nonterminal, was not found in name map.) (Residue 159: ASP, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: THR, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: VAL, Nonterminal, was not found in name map.) (Residue 165: GLY, Nonterminal, was not found in name map.) (Residue 166: GLN, Nonterminal, was not found in name map.) (Residue 167: MET, Nonterminal, was not found in name map.) (Residue 168: TYR, Nonterminal, was not found in name map.) (Residue 169: ASP, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: THR, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: MET, Nonterminal, was not found in name map.) (Residue 174: CYS, 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: ASN, Nonterminal, was not found in name map.) (Residue 178: LYS, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: ASP, Nonterminal, was not found in name map.) (Residue 181: PRO, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: VAL, Nonterminal, was not found in name map.) (Residue 184: ALA, Nonterminal, was not found in name map.) (Residue 185: GLN, Nonterminal, was not found in name map.) (Residue 186: PRO, Nonterminal, was not found in name map.) (Residue 187: MET, Nonterminal, was not found in name map.) (Residue 188: THR, Nonterminal, was not found in name map.) (Residue 189: THR, Nonterminal, was not found in name map.) (Residue 190: ASP, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: GLU, Nonterminal, was not found in name map.) (Residue 194: PHE, Nonterminal, was not found in name map.) (Residue 195: THR, Nonterminal, was not found in name map.) (Residue 196: PRO, Nonterminal, was not found in name map.) (Residue 197: ALA, Nonterminal, was not found in name map.) (Residue 198: ILE, Nonterminal, was not found in name map.) (Residue 199: TYR, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: ARG, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: VAL, Nonterminal, was not found in name map.) (Residue 204: LYS, Nonterminal, was not found in name map.) (Residue 205: TYR, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 206 to: CLYS. Mapped residue THR, term: Terminal/beginning, seq. number: 207 to: NTHR. (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: TYR, Nonterminal, was not found in name map.) (Residue 211: THR, Nonterminal, was not found in name map.) (Residue 212: TYR, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: PRO, Nonterminal, was not found in name map.) (Residue 216: LEU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: MET, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: VAL, Nonterminal, was not found in name map.) (Residue 223: SER, Nonterminal, was not found in name map.) (Residue 224: GLU, Nonterminal, was not found in name map.) (Residue 225: ALA, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: ALA, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: VAL, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: MET, Nonterminal, was not found in name map.) (Residue 232: ASN, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: ARG, Nonterminal, was not found in name map.) (Residue 237: VAL, Nonterminal, was not found in name map.) (Residue 238: ALA, Nonterminal, was not found in name map.) (Residue 239: HIS, Nonterminal, was not found in name map.) (Residue 240: LEU, Nonterminal, was not found in name map.) (Residue 241: ILE, Nonterminal, was not found in name map.) (Residue 242: GLY, Nonterminal, was not found in name map.) (Residue 243: GLU, Nonterminal, was not found in name map.) (Residue 244: TYR, Nonterminal, was not found in name map.) (Residue 245: PHE, Nonterminal, was not found in name map.) (Residue 246: GLN, Nonterminal, was not found in name map.) (Residue 247: VAL, Nonterminal, was not found in name map.) (Residue 248: GLN, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 249 to: CASP. Mapped residue ASP, term: Terminal/beginning, seq. number: 250 to: NASP. (Residue 251: VAL, Nonterminal, was not found in name map.) (Residue 252: MET, Nonterminal, was not found in name map.) (Residue 253: ASP, Nonterminal, was not found in name map.) (Residue 254: CYS, Nonterminal, was not found in name map.) (Residue 255: PHE, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: PRO, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: GLN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: GLY, Nonterminal, was not found in name map.) (Residue 263: LYS, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: GLY, Nonterminal, was not found in name map.) (Residue 266: THR, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: ILE, Nonterminal, was not found in name map.) (Residue 269: GLU, Nonterminal, was not found in name map.) (Residue 270: ASP, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: LYS, Nonterminal, was not found in name map.) (Residue 273: CYS, Nonterminal, was not found in name map.) (Residue 274: SER, Nonterminal, was not found in name map.) (Residue 275: TRP, Nonterminal, was not found in name map.) (Residue 276: LEU, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: VAL, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: PHE, Nonterminal, was not found in name map.) (Residue 281: LEU, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: LYS, Nonterminal, was not found in name map.) (Residue 284: ALA, Nonterminal, was not found in name map.) (Residue 285: ASN, Nonterminal, was not found in name map.) (Residue 286: ALA, Nonterminal, was not found in name map.) (Residue 287: ALA, Nonterminal, was not found in name map.) (Residue 288: GLN, Nonterminal, was not found in name map.) (Residue 289: VAL, Nonterminal, was not found in name map.) (Residue 290: ALA, Nonterminal, was not found in name map.) (Residue 291: GLU, Nonterminal, was not found in name map.) (Residue 292: PHE, Nonterminal, was not found in name map.) (Residue 293: LYS, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: ASN, Nonterminal, was not found in name map.) (Residue 296: TYR, Nonterminal, was not found in name map.) (Residue 297: GLY, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: LYS, Nonterminal, was not found in name map.) (Residue 300: ASP, Nonterminal, was not found in name map.) (Residue 301: PRO, Nonterminal, was not found in name map.) (Residue 302: ALA, Nonterminal, was not found in name map.) (Residue 303: LYS, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ALA, Nonterminal, was not found in name map.) (Residue 306: VAL, Nonterminal, was not found in name map.) (Residue 307: VAL, Nonterminal, was not found in name map.) (Residue 308: LYS, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: LEU, Nonterminal, was not found in name map.) (Residue 311: TYR, Nonterminal, was not found in name map.) (Residue 312: SER, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: ALA, Nonterminal, was not found in name map.) (Residue 315: ASN, Nonterminal, was not found in name map.) (Residue 316: LEU, Nonterminal, was not found in name map.) (Residue 317: GLN, Nonterminal, was not found in name map.) (Residue 318: ALA, Nonterminal, was not found in name map.) (Residue 319: ASP, Nonterminal, was not found in name map.) (Residue 320: PHE, Nonterminal, was not found in name map.) (Residue 321: ALA, Nonterminal, was not found in name map.) (Residue 322: ALA, Nonterminal, was not found in name map.) (Residue 323: TYR, Nonterminal, was not found in name map.) (Residue 324: GLU, Nonterminal, was not found in name map.) (Residue 325: ALA, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: VAL, Nonterminal, was not found in name map.) (Residue 328: VAL, Nonterminal, was not found in name map.) (Residue 329: ARG, Nonterminal, was not found in name map.) (Residue 330: GLU, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: GLU, Nonterminal, was not found in name map.) (Residue 333: SER, Nonterminal, was not found in name map.) (Residue 334: LEU, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: GLU, Nonterminal, was not found in name map.) (Residue 337: GLN, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: LYS, Nonterminal, was not found in name map.) (Residue 340: VAL, Nonterminal, was not found in name map.) (Residue 341: LYS, Nonterminal, was not found in name map.) (Residue 342: SER, Nonterminal, was not found in name map.) (Residue 343: PRO, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: PHE, Nonterminal, was not found in name map.) (Residue 346: ALA, Nonterminal, was not found in name map.) (Residue 347: GLU, Nonterminal, was not found in name map.) (Residue 348: SER, Nonterminal, was not found in name map.) (Residue 349: VAL, Nonterminal, was not found in name map.) (Residue 350: ALA, Nonterminal, was not found in name map.) (Residue 351: VAL, Nonterminal, was not found in name map.) (Residue 352: VAL, Nonterminal, was not found in name map.) (Residue 353: TRP, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: LYS, Nonterminal, was not found in name map.) (Residue 356: THR, Nonterminal, was not found in name map.) (Residue 357: HIS, Nonterminal, was not found in name map.) (Residue 358: LYS, Nonterminal, was not found in name map.) (Residue 359: ARG, Nonterminal, was not found in name map.) (Residue 360: LYS, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 361 to: CLYS. (Residue 362: A0N, Terminal/beginning, was not found in name map.) Unknown residue: A0N number: 362 type: Terminal/beginning ..relaxing end constraints to try for a dbase match -no luck (Residue 363: DMA, Nonterminal, was not found in name map.) Unknown residue: DMA number: 363 type: Nonterminal (Residue 364: MG2, Nonterminal, was not found in name map.) (Residue 365: MG2, Nonterminal, was not found in name map.) (Residue 366: MG2, Nonterminal, was not found in name map.) (Residue 367: SO4, Nonterminal, was not found in name map.) Unknown residue: SO4 number: 367 type: Nonterminal (Residue 368: HOH, Nonterminal, was not found in name map.) (Residue 369: HOH, Nonterminal, was not found in name map.) (Residue 370: HOH, Nonterminal, was not found in name map.) (Residue 371: HOH, Nonterminal, was not found in name map.) (Residue 372: HOH, Nonterminal, was not found in name map.) (Residue 373: HOH, Nonterminal, was not found in name map.) (Residue 374: HOH, Nonterminal, was not found in name map.) (Residue 375: HOH, Nonterminal, was not found in name map.) (Residue 376: HOH, Nonterminal, was not found in name map.) (Residue 377: HOH, Nonterminal, was not found in name map.) (Residue 378: HOH, Nonterminal, was not found in name map.) (Residue 379: HOH, Nonterminal, was not found in name map.) (Residue 380: HOH, Nonterminal, was not found in name map.) (Residue 381: HOH, Nonterminal, was not found in name map.) (Residue 382: HOH, Nonterminal, was not found in name map.) (Residue 383: HOH, Nonterminal, was not found in name map.) (Residue 384: HOH, Nonterminal, was not found in name map.) (Residue 385: HOH, Nonterminal, was not found in name map.) (Residue 386: HOH, Nonterminal, was not found in name map.) (Residue 387: HOH, Nonterminal, was not found in name map.) (Residue 388: HOH, Nonterminal, was not found in name map.) (Residue 389: HOH, Nonterminal, was not found in name map.) (Residue 390: HOH, Nonterminal, was not found in name map.) (Residue 391: HOH, Nonterminal, was not found in name map.) (Residue 392: HOH, Nonterminal, was not found in name map.) (Residue 393: HOH, Nonterminal, was not found in name map.) (Residue 394: HOH, Nonterminal, was not found in name map.) (Residue 395: HOH, Nonterminal, was not found in name map.) (Residue 396: HOH, Nonterminal, was not found in name map.) (Residue 397: HOH, Nonterminal, was not found in name map.) (Residue 398: HOH, Nonterminal, was not found in name map.) (Residue 399: HOH, Nonterminal, was not found in name map.) (Residue 400: HOH, Nonterminal, was not found in name map.) (Residue 401: HOH, Nonterminal, was not found in name map.) (Residue 402: HOH, Nonterminal, was not found in name map.) (Residue 403: HOH, Nonterminal, was not found in name map.) (Residue 404: HOH, Nonterminal, was not found in name map.) (Residue 405: HOH, Nonterminal, was not found in name map.) (Residue 406: HOH, Nonterminal, was not found in name map.) (Residue 407: HOH, Nonterminal, was not found in name map.) (Residue 408: HOH, Nonterminal, was not found in name map.) (Residue 409: HOH, Nonterminal, was not found in name map.) (Residue 410: HOH, Nonterminal, was not found in name map.) (Residue 411: HOH, Nonterminal, was not found in name map.) (Residue 412: HOH, Nonterminal, was not found in name map.) (Residue 413: HOH, Nonterminal, was not found in name map.) (Residue 414: HOH, Nonterminal, was not found in name map.) (Residue 415: HOH, Nonterminal, was not found in name map.) (Residue 416: HOH, Nonterminal, was not found in name map.) (Residue 417: HOH, Nonterminal, was not found in name map.) (Residue 418: HOH, Nonterminal, was not found in name map.) (Residue 419: HOH, Nonterminal, was not found in name map.) (Residue 420: HOH, Nonterminal, was not found in name map.) (Residue 421: HOH, Nonterminal, was not found in name map.) (Residue 422: HOH, Nonterminal, was not found in name map.) (Residue 423: HOH, Nonterminal, was not found in name map.) (Residue 424: HOH, Nonterminal, was not found in name map.) (Residue 425: HOH, Nonterminal, was not found in name map.) (Residue 426: HOH, Nonterminal, was not found in name map.) (Residue 427: HOH, Nonterminal, was not found in name map.) (Residue 428: HOH, Nonterminal, was not found in name map.) (Residue 429: HOH, Nonterminal, was not found in name map.) (Residue 430: HOH, Nonterminal, was not found in name map.) (Residue 431: HOH, Nonterminal, was not found in name map.) (Residue 432: HOH, Nonterminal, was not found in name map.) (Residue 433: HOH, Nonterminal, was not found in name map.) (Residue 434: HOH, Nonterminal, was not found in name map.) (Residue 435: HOH, Nonterminal, was not found in name map.) (Residue 436: HOH, Nonterminal, was not found in name map.) (Residue 437: HOH, Nonterminal, was not found in name map.) (Residue 438: HOH, Nonterminal, was not found in name map.) (Residue 439: HOH, Nonterminal, was not found in name map.) (Residue 440: HOH, Nonterminal, was not found in name map.) (Residue 441: HOH, Nonterminal, was not found in name map.) (Residue 442: HOH, Nonterminal, was not found in name map.) (Residue 443: HOH, Nonterminal, was not found in name map.) (Residue 444: HOH, Nonterminal, was not found in name map.) (Residue 445: HOH, Nonterminal, was not found in name map.) (Residue 446: HOH, Nonterminal, was not found in name map.) (Residue 447: HOH, Nonterminal, was not found in name map.) (Residue 448: HOH, Nonterminal, was not found in name map.) (Residue 449: HOH, Nonterminal, was not found in name map.) (Residue 450: HOH, Nonterminal, was not found in name map.) (Residue 451: HOH, Nonterminal, was not found in name map.) (Residue 452: HOH, Nonterminal, was not found in name map.) (Residue 453: HOH, Nonterminal, was not found in name map.) (Residue 454: HOH, Nonterminal, was not found in name map.) (Residue 455: HOH, Nonterminal, was not found in name map.) (Residue 456: HOH, Nonterminal, was not found in name map.) (Residue 457: HOH, Nonterminal, was not found in name map.) (Residue 458: HOH, Nonterminal, was not found in name map.) (Residue 459: HOH, Nonterminal, was not found in name map.) (Residue 460: HOH, Nonterminal, was not found in name map.) (Residue 461: HOH, Nonterminal, was not found in name map.) (Residue 462: HOH, Nonterminal, was not found in name map.) (Residue 463: HOH, Nonterminal, was not found in name map.) (Residue 464: HOH, Nonterminal, was not found in name map.) (Residue 465: HOH, Nonterminal, was not found in name map.) (Residue 466: HOH, Nonterminal, was not found in name map.) (Residue 467: HOH, Nonterminal, was not found in name map.) (Residue 468: HOH, Nonterminal, was not found in name map.) (Residue 469: HOH, Nonterminal, was not found in name map.) (Residue 470: HOH, Nonterminal, was not found in name map.) (Residue 471: HOH, Nonterminal, was not found in name map.) (Residue 472: HOH, Nonterminal, was not found in name map.) (Residue 473: HOH, Nonterminal, was not found in name map.) (Residue 474: HOH, Nonterminal, was not found in name map.) (Residue 475: HOH, Nonterminal, was not found in name map.) (Residue 476: HOH, Nonterminal, was not found in name map.) (Residue 477: HOH, Nonterminal, was not found in name map.) (Residue 478: HOH, Nonterminal, was not found in name map.) (Residue 479: HOH, Nonterminal, was not found in name map.) (Residue 480: HOH, Nonterminal, was not found in name map.) (Residue 481: HOH, Nonterminal, was not found in name map.) (Residue 482: HOH, Nonterminal, was not found in name map.) (Residue 483: HOH, Nonterminal, was not found in name map.) (Residue 484: HOH, Nonterminal, was not found in name map.) (Residue 485: HOH, Nonterminal, was not found in name map.) (Residue 486: HOH, Nonterminal, was not found in name map.) (Residue 487: HOH, Nonterminal, was not found in name map.) (Residue 488: HOH, Nonterminal, was not found in name map.) (Residue 489: HOH, Nonterminal, was not found in name map.) (Residue 490: HOH, Nonterminal, was not found in name map.) (Residue 491: HOH, Nonterminal, was not found in name map.) (Residue 492: HOH, Nonterminal, was not found in name map.) (Residue 493: HOH, Nonterminal, was not found in name map.) (Residue 494: HOH, Nonterminal, was not found in name map.) (Residue 495: HOH, Nonterminal, was not found in name map.) (Residue 496: HOH, Nonterminal, was not found in name map.) (Residue 497: HOH, Nonterminal, was not found in name map.) (Residue 498: HOH, Nonterminal, was not found in name map.) (Residue 499: HOH, Nonterminal, was not found in name map.) (Residue 500: HOH, Nonterminal, was not found in name map.) (Residue 501: HOH, Nonterminal, was not found in name map.) (Residue 502: HOH, Nonterminal, was not found in name map.) (Residue 503: HOH, Nonterminal, was not found in name map.) (Residue 504: HOH, Nonterminal, was not found in name map.) (Residue 505: HOH, Nonterminal, was not found in name map.) (Residue 506: HOH, Nonterminal, was not found in name map.) (Residue 507: HOH, Nonterminal, was not found in name map.) (Residue 508: HOH, Nonterminal, was not found in name map.) (Residue 509: HOH, Nonterminal, was not found in name map.) (Residue 510: HOH, Nonterminal, was not found in name map.) (Residue 511: HOH, Nonterminal, was not found in name map.) (Residue 512: HOH, Nonterminal, was not found in name map.) (Residue 513: HOH, Nonterminal, was not found in name map.) (Residue 514: HOH, Nonterminal, was not found in name map.) (Residue 515: HOH, Nonterminal, was not found in name map.) (Residue 516: HOH, Nonterminal, was not found in name map.) (Residue 517: HOH, Nonterminal, was not found in name map.) (Residue 518: HOH, Nonterminal, was not found in name map.) (Residue 519: HOH, Nonterminal, was not found in name map.) (Residue 520: HOH, Nonterminal, was not found in name map.) (Residue 521: HOH, Nonterminal, was not found in name map.) (Residue 522: HOH, Nonterminal, was not found in name map.) (Residue 523: HOH, Nonterminal, was not found in name map.) (Residue 524: HOH, Nonterminal, was not found in name map.) (Residue 525: HOH, Nonterminal, was not found in name map.) (Residue 526: HOH, Nonterminal, was not found in name map.) (Residue 527: HOH, Nonterminal, was not found in name map.) (Residue 528: HOH, Nonterminal, was not found in name map.) (Residue 529: HOH, Nonterminal, was not found in name map.) (Residue 530: HOH, Nonterminal, was not found in name map.) (Residue 531: HOH, Nonterminal, was not found in name map.) (Residue 532: HOH, Nonterminal, was not found in name map.) (Residue 533: HOH, Nonterminal, was not found in name map.) (Residue 534: HOH, Nonterminal, was not found in name map.) (Residue 535: HOH, Nonterminal, was not found in name map.) (Residue 536: HOH, Nonterminal, was not found in name map.) (Residue 537: HOH, Nonterminal, was not found in name map.) (Residue 538: HOH, Nonterminal, was not found in name map.) (Residue 539: HOH, Nonterminal, was not found in name map.) (Residue 540: HOH, Nonterminal, was not found in name map.) (Residue 541: HOH, Nonterminal, was not found in name map.) (Residue 542: HOH, Nonterminal, was not found in name map.) (Residue 543: HOH, Nonterminal, was not found in name map.) (Residue 544: HOH, Nonterminal, was not found in name map.) (Residue 545: HOH, Nonterminal, was not found in name map.) (Residue 546: HOH, Nonterminal, was not found in name map.) (Residue 547: HOH, Nonterminal, was not found in name map.) (Residue 548: HOH, Nonterminal, was not found in name map.) (Residue 549: HOH, Nonterminal, was not found in name map.) (Residue 550: HOH, Nonterminal, was not found in name map.) (Residue 551: HOH, Nonterminal, was not found in name map.) (Residue 552: HOH, Nonterminal, was not found in name map.) (Residue 553: HOH, Nonterminal, was not found in name map.) (Residue 554: HOH, Nonterminal, was not found in name map.) (Residue 555: HOH, Nonterminal, was not found in name map.) (Residue 556: HOH, Nonterminal, was not found in name map.) (Residue 557: HOH, Nonterminal, was not found in name map.) (Residue 558: HOH, Nonterminal, was not found in name map.) (Residue 559: HOH, Nonterminal, was not found in name map.) (Residue 560: HOH, Nonterminal, was not found in name map.) (Residue 561: HOH, Nonterminal, was not found in name map.) (Residue 562: HOH, Nonterminal, was not found in name map.) (Residue 563: HOH, Nonterminal, was not found in name map.) (Residue 564: HOH, Nonterminal, was not found in name map.) (Residue 565: HOH, Nonterminal, was not found in name map.) (Residue 566: HOH, Nonterminal, was not found in name map.) (Residue 567: HOH, Nonterminal, was not found in name map.) (Residue 568: HOH, Nonterminal, was not found in name map.) (Residue 569: HOH, Nonterminal, was not found in name map.) (Residue 570: HOH, Nonterminal, was not found in name map.) (Residue 571: HOH, Nonterminal, was not found in name map.) (Residue 572: HOH, Nonterminal, was not found in name map.) (Residue 573: HOH, Nonterminal, was not found in name map.) (Residue 574: HOH, Nonterminal, was not found in name map.) (Residue 575: HOH, Nonterminal, was not found in name map.) (Residue 576: HOH, Nonterminal, was not found in name map.) (Residue 577: HOH, Nonterminal, was not found in name map.) (Residue 578: HOH, Nonterminal, was not found in name map.) (Residue 579: HOH, Nonterminal, was not found in name map.) (Residue 580: HOH, Nonterminal, was not found in name map.) (Residue 581: HOH, Nonterminal, was not found in name map.) (Residue 582: HOH, Nonterminal, was not found in name map.) (Residue 583: HOH, Nonterminal, was not found in name map.) (Residue 584: HOH, Nonterminal, was not found in name map.) (Residue 585: HOH, Nonterminal, was not found in name map.) (Residue 586: HOH, Nonterminal, was not found in name map.) (Residue 587: HOH, Nonterminal, was not found in name map.) (Residue 588: HOH, Nonterminal, was not found in name map.) (Residue 589: HOH, Nonterminal, was not found in name map.) (Residue 590: HOH, Nonterminal, was not found in name map.) (Residue 591: HOH, Nonterminal, was not found in name map.) (Residue 592: HOH, Nonterminal, was not found in name map.) (Residue 593: HOH, Nonterminal, was not found in name map.) (Residue 594: HOH, Nonterminal, was not found in name map.) (Residue 595: HOH, Nonterminal, was not found in name map.) (Residue 596: HOH, Nonterminal, was not found in name map.) (Residue 597: HOH, Nonterminal, was not found in name map.) (Residue 598: HOH, Nonterminal, was not found in name map.) (Residue 599: HOH, Nonterminal, was not found in name map.) (Residue 600: HOH, Nonterminal, was not found in name map.) (Residue 601: HOH, Nonterminal, was not found in name map.) (Residue 602: HOH, Nonterminal, was not found in name map.) (Residue 603: HOH, Nonterminal, was not found in name map.) (Residue 604: HOH, Nonterminal, was not found in name map.) (Residue 605: HOH, Nonterminal, was not found in name map.) (Residue 606: HOH, Nonterminal, was not found in name map.) (Residue 607: HOH, Nonterminal, was not found in name map.) (Residue 608: HOH, Nonterminal, was not found in name map.) (Residue 609: HOH, Nonterminal, was not found in name map.) (Residue 610: HOH, Nonterminal, was not found in name map.) (Residue 611: HOH, Nonterminal, was not found in name map.) (Residue 612: HOH, Nonterminal, was not found in name map.) (Residue 613: HOH, Nonterminal, was not found in name map.) (Residue 614: HOH, Nonterminal, was not found in name map.) (Residue 615: HOH, Nonterminal, was not found in name map.) (Residue 616: HOH, Nonterminal, was not found in name map.) (Residue 617: HOH, Nonterminal, was not found in name map.) (Residue 618: HOH, Nonterminal, was not found in name map.) (Residue 619: HOH, Nonterminal, was not found in name map.) (Residue 620: HOH, Nonterminal, was not found in name map.) (Residue 621: HOH, Nonterminal, was not found in name map.) (Residue 622: HOH, Nonterminal, was not found in name map.) (Residue 623: HOH, Nonterminal, was not found in name map.) (Residue 624: HOH, Nonterminal, was not found in name map.) (Residue 625: HOH, Nonterminal, was not found in name map.) (Residue 626: HOH, Nonterminal, was not found in name map.) (Residue 627: HOH, Nonterminal, was not found in name map.) (Residue 628: HOH, Nonterminal, was not found in name map.) (Residue 629: HOH, Nonterminal, was not found in name map.) (Residue 630: HOH, Nonterminal, was not found in name map.) (Residue 631: HOH, Nonterminal, was not found in name map.) (Residue 632: HOH, Nonterminal, was not found in name map.) (Residue 633: HOH, Nonterminal, was not found in name map.) (Residue 634: HOH, Nonterminal, was not found in name map.) (Residue 635: HOH, Nonterminal, was not found in name map.) (Residue 636: HOH, Nonterminal, was not found in name map.) (Residue 637: HOH, Nonterminal, was not found in name map.) (Residue 638: HOH, Nonterminal, was not found in name map.) (Residue 639: HOH, Nonterminal, was not found in name map.) (Residue 640: HOH, Nonterminal, was not found in name map.) (Residue 641: HOH, Nonterminal, was not found in name map.) (Residue 642: HOH, Nonterminal, was not found in name map.) (Residue 643: HOH, Nonterminal, was not found in name map.) (Residue 644: HOH, Nonterminal, was not found in name map.) (Residue 645: HOH, Nonterminal, was not found in name map.) (Residue 646: HOH, Nonterminal, was not found in name map.) (Residue 647: HOH, Nonterminal, was not found in name map.) (Residue 648: HOH, Nonterminal, was not found in name map.) (Residue 649: HOH, Nonterminal, was not found in name map.) (Residue 650: HOH, Nonterminal, was not found in name map.) (Residue 651: HOH, Nonterminal, was not found in name map.) (Residue 652: HOH, Nonterminal, was not found in name map.) (Residue 653: HOH, Nonterminal, was not found in name map.) (Residue 654: HOH, Nonterminal, was not found in name map.) (Residue 655: HOH, Nonterminal, was not found in name map.) (Residue 656: HOH, Nonterminal, was not found in name map.) (Residue 657: HOH, Nonterminal, was not found in name map.) (Residue 658: HOH, Nonterminal, was not found in name map.) (Residue 659: HOH, Nonterminal, was not found in name map.) (Residue 660: HOH, Nonterminal, was not found in name map.) (Residue 661: HOH, Nonterminal, was not found in name map.) (Residue 662: HOH, Nonterminal, was not found in name map.) (Residue 663: HOH, Nonterminal, was not found in name map.) (Residue 664: HOH, Nonterminal, was not found in name map.) (Residue 665: HOH, Nonterminal, was not found in name map.) (Residue 666: HOH, Nonterminal, was not found in name map.) (Residue 667: HOH, Nonterminal, was not found in name map.) (Residue 668: HOH, Nonterminal, was not found in name map.) (Residue 669: HOH, Nonterminal, was not found in name map.) (Residue 670: HOH, Nonterminal, was not found in name map.) (Residue 671: HOH, Nonterminal, was not found in name map.) (Residue 672: HOH, Nonterminal, was not found in name map.) (Residue 673: HOH, Nonterminal, was not found in name map.) (Residue 674: HOH, Nonterminal, was not found in name map.) (Residue 675: HOH, Nonterminal, was not found in name map.) (Residue 676: HOH, Nonterminal, was not found in name map.) (Residue 677: HOH, Nonterminal, was not found in name map.) (Residue 678: HOH, Nonterminal, was not found in name map.) (Residue 679: HOH, Nonterminal, was not found in name map.) (Residue 680: HOH, Nonterminal, was not found in name map.) (Residue 681: HOH, Nonterminal, was not found in name map.) (Residue 682: HOH, Nonterminal, was not found in name map.) (Residue 683: HOH, Nonterminal, was not found in name map.) (Residue 684: HOH, Nonterminal, was not found in name map.) (Residue 685: HOH, Nonterminal, was not found in name map.) (Residue 686: HOH, Nonterminal, was not found in name map.) (Residue 687: HOH, Nonterminal, was not found in name map.) (Residue 688: HOH, Nonterminal, was not found in name map.) (Residue 689: HOH, Nonterminal, was not found in name map.) (Residue 690: HOH, Nonterminal, was not found in name map.) (Residue 691: HOH, Nonterminal, was not found in name map.) (Residue 692: HOH, Nonterminal, was not found in name map.) (Residue 693: HOH, Nonterminal, was not found in name map.) (Residue 694: HOH, Nonterminal, was not found in name map.) (Residue 695: HOH, Nonterminal, was not found in name map.) (Residue 696: HOH, Nonterminal, was not found in name map.) (Residue 697: HOH, Nonterminal, was not found in name map.) (Residue 698: HOH, Nonterminal, was not found in name map.) (Residue 699: HOH, Nonterminal, was not found in name map.) (Residue 700: HOH, Nonterminal, was not found in name map.) (Residue 701: HOH, Nonterminal, was not found in name map.) (Residue 702: HOH, Nonterminal, was not found in name map.) (Residue 703: HOH, Nonterminal, was not found in name map.) (Residue 704: HOH, Nonterminal, was not found in name map.) (Residue 705: HOH, Nonterminal, was not found in name map.) (Residue 706: HOH, Nonterminal, was not found in name map.) (Residue 707: HOH, Nonterminal, was not found in name map.) (Residue 708: HOH, Nonterminal, was not found in name map.) (Residue 709: HOH, Nonterminal, was not found in name map.) (Residue 710: HOH, Nonterminal, was not found in name map.) (Residue 711: HOH, Nonterminal, was not found in name map.) (Residue 712: HOH, Nonterminal, was not found in name map.) (Residue 713: HOH, Nonterminal, was not found in name map.) (Residue 714: HOH, Nonterminal, was not found in name map.) (Residue 715: HOH, Nonterminal, was not found in name map.) (Residue 716: HOH, Nonterminal, was not found in name map.) (Residue 717: HOH, Nonterminal, was not found in name map.) (Residue 718: HOH, Nonterminal, was not found in name map.) (Residue 719: HOH, Nonterminal, was not found in name map.) (Residue 720: HOH, Nonterminal, was not found in name map.) (Residue 721: HOH, Nonterminal, was not found in name map.) (Residue 722: HOH, Nonterminal, was not found in name map.) (Residue 723: HOH, Nonterminal, was not found in name map.) (Residue 724: HOH, Nonterminal, was not found in name map.) (Residue 725: HOH, Nonterminal, was not found in name map.) (Residue 726: HOH, Nonterminal, was not found in name map.) (Residue 727: HOH, Nonterminal, was not found in name map.) (Residue 728: HOH, Nonterminal, was not found in name map.) (Residue 729: HOH, Nonterminal, was not found in name map.) (Residue 730: HOH, Nonterminal, was not found in name map.) (Residue 731: HOH, Nonterminal, was not found in name map.) (Residue 732: HOH, Nonterminal, was not found in name map.) (Residue 733: HOH, Nonterminal, was not found in name map.) (Residue 734: HOH, Nonterminal, was not found in name map.) (Residue 735: HOH, Nonterminal, was not found in name map.) (Residue 736: HOH, Nonterminal, was not found in name map.) (Residue 737: HOH, Nonterminal, was not found in name map.) (Residue 738: HOH, Nonterminal, was not found in name map.) (Residue 739: HOH, Nonterminal, was not found in name map.) (Residue 740: HOH, Nonterminal, was not found in name map.) (Residue 741: HOH, Nonterminal, was not found in name map.) (Residue 742: HOH, Nonterminal, was not found in name map.) (Residue 743: HOH, Nonterminal, was not found in name map.) (Residue 744: HOH, Nonterminal, was not found in name map.) (Residue 745: HOH, Nonterminal, was not found in name map.) (Residue 746: HOH, Nonterminal, was not found in name map.) (Residue 747: HOH, Nonterminal, was not found in name map.) (Residue 748: HOH, Nonterminal, was not found in name map.) (Residue 749: HOH, Nonterminal, was not found in name map.) (Residue 750: HOH, Nonterminal, was not found in name map.) (Residue 751: HOH, Nonterminal, was not found in name map.) (Residue 752: HOH, Nonterminal, was not found in name map.) (Residue 753: HOH, Nonterminal, was not found in name map.) (Residue 754: HOH, Nonterminal, was not found in name map.) (Residue 755: HOH, Nonterminal, was not found in name map.) (Residue 756: HOH, Nonterminal, was not found in name map.) (Residue 757: HOH, Nonterminal, was not found in name map.) (Residue 758: HOH, Nonterminal, was not found in name map.) (Residue 759: HOH, Terminal/last, was not found in name map.) Joining NMET - ALA Joining ALA - SER Joining SER - MET Joining MET - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - SER Joining SER - VAL Joining VAL - TYR Joining TYR - ASP Joining ASP - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - GLN Joining GLN - SER Joining SER - LYS Joining LYS - TYR Joining TYR - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - ASN Joining ASN - ARG Joining ARG - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - MET Joining MET - MET Joining MET - ASP Joining ASP - THR Joining THR - THR Joining THR - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - PHE Joining PHE - ARG Joining ARG - GLY Joining GLY - MET Joining MET - THR Joining THR - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - VAL Joining VAL - THR Joining THR - GLN Joining GLN - HIE Joining HIE - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - THR Joining THR - LYS Joining LYS - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - ALA Joining ALA - CYS Joining CYS - VAL Joining VAL - GLY Joining GLY - GLY Joining GLY - TRP Joining TRP - MET Joining MET - ILE Joining ILE - GLU Joining GLU - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - CTYR Added missing heavy atom: .R.A Joining NLEU - VAL Joining VAL - GLU Joining GLU - CASP Added missing heavy atom: .R.A Joining NASP - ILE Joining ILE - MET Joining MET - ASP Joining ASP - GLY Joining GLY - SER Joining SER - VAL Joining VAL - MET Joining MET - ARG Joining ARG - ARG Joining ARG - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - TRP Joining TRP - TYR Joining TYR - ARG Joining ARG - PHE Joining PHE - PRO Joining PRO - GLY Joining GLY - VAL Joining VAL - THR Joining THR - THR Joining THR - GLN Joining GLN - CYS Joining CYS - ALA Joining ALA - ILE Joining ILE - ASN Joining ASN - ASP Joining ASP - GLY Joining GLY - ILE Joining ILE - ILE Joining ILE - LEU Joining LEU - LYS Joining LYS - SER Joining SER - TRP Joining TRP - THR Joining THR - GLN Joining GLN - ILE Joining ILE - MET Joining MET - ALA Joining ALA - TRP Joining TRP - HIE Joining HIE - TYR Joining TYR - PHE Joining PHE - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - LEU Joining LEU - LEU Joining LEU - CYS Joining CYS - LEU Joining LEU - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - VAL Joining VAL - ASP Joining ASP - TYR Joining TYR - ALA Joining ALA - THR Joining THR - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - GLN Joining GLN - MET Joining MET - TYR Joining TYR - ASP Joining ASP - VAL Joining VAL - THR Joining THR - SER Joining SER - MET Joining MET - CYS Joining CYS - ASP Joining ASP - SER Joining SER - ASN Joining ASN - LYS Joining LYS - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - MET Joining MET - THR Joining THR - THR Joining THR - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - GLU Joining GLU - PHE Joining PHE - THR Joining THR - PRO Joining PRO - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - LYS Joining LYS - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - LYS Joining LYS - TYR Joining TYR - CLYS Added missing heavy atom: .R.A Joining NTHR - THR Joining THR - PHE Joining PHE - TYR Joining TYR - THR Joining THR - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - VAL Joining VAL - MET Joining MET - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - VAL Joining VAL - SER Joining SER - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - GLU Joining GLU - MET Joining MET - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - HIE Joining HIE - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - GLU Joining GLU - TYR Joining TYR - PHE Joining PHE - GLN Joining GLN - VAL Joining VAL - GLN Joining GLN - CASP Added missing heavy atom: .R.A Joining NASP - VAL Joining VAL - MET Joining MET - ASP Joining ASP - CYS Joining CYS - PHE Joining PHE - THR Joining THR - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - GLN Joining GLN - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - THR Joining THR - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - ALA Joining ALA - LYS Joining LYS - CYS Joining CYS - SER Joining SER - TRP Joining TRP - LEU Joining LEU - ALA Joining ALA - VAL Joining VAL - THR Joining THR - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - PHE Joining PHE - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - TYR Joining TYR - SER Joining SER - GLU Joining GLU - ALA Joining ALA - ASN Joining ASN - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - ALA Joining ALA - TYR Joining TYR - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - LYS Joining LYS - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - ALA Joining ALA - GLU Joining GLU - SER Joining SER - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - THR Joining THR - HIE Joining HIE - LYS Joining LYS - ARG Joining ARG - LYS Joining LYS - CLYS Added missing heavy atom: .R.A Creating new UNIT for residue: A0N sequence: 363 Created a new atom named: CAG within residue: .R Created a new atom named: NAI within residue: .R Created a new atom named: CAK within residue: .R Created a new atom named: CAH within residue: .R Created a new atom named: CAF within residue: .R Created a new atom named: CAE within residue: .R Created a new atom named: CAL within residue: .R Created a new atom named: CAJ within residue: .R Created a new atom named: CAA within residue: .R Created a new atom named: CAD within residue: .R Created a new atom named: OAC within residue: .R Created a new atom named: NAB within residue: .R Created a new atom named: H004 within residue: .R Created a new atom named: H001 within residue: .R Created a new atom named: H002 within residue: .R Created a new atom named: H003 within residue: .R Created a new atom named: H005 within residue: .R Created a new atom named: H007 within residue: .R Created a new atom named: H006 within residue: .R Created a new atom named: HAA within residue: .R Creating new UNIT for residue: DMA sequence: 364 Starting new chain with Created a new atom named: C1 within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: PA within residue: .R Created a new atom named: O1A within residue: .R Created a new atom named: O2A within residue: .R Created a new atom named: O3A within residue: .R Created a new atom named: PB within residue: .R Created a new atom named: O1B within residue: .R Created a new atom named: O2B within residue: .R Created a new atom named: O3B within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: H12 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H41 within residue: .R Created a new atom named: H42 within residue: .R Created a new atom named: H43 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Created a new atom named: H1B within residue: .R Starting new chain with MG2 Starting new chain with MG2 Starting new chain with MG2 Creating new UNIT for residue: SO4 sequence: 368 Starting new chain with Created a new atom named: S within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: O3 within residue: .R Created a new atom named: O4 within residue: .R Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 total atoms in file: 3335 Leap added 3653 missing atoms according to residue templates: 5 Heavy 3648 H / lone pairs The file contained 49 atoms not in residue templates > saveamberparm pront 1yhl_a0n.prmtop 1yhl_a0n.prmcrd saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > saveamberparm prot 1yhl_a0n.prmtop 1yhl_a0n.prmcrd Checking Unit. WARNING: The unperturbed charge of the unit: -5.000000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. log started: Fri May 29 16:26:33 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> 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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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: /opt/amber9/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 > > atomtypes ERROR: syntax error