log started: Mon Apr 25 19:36:35 2005 Log file: ./leap.log >> # >> # ----- leaprc for loading the parm99 additive force field, no lone pairs >> # assumes that any unspecified nucleic acids are DNA >> # >> # 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" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /usr/local/amber8/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_amino94.lib Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib 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: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff all_aminoct94.lib Loading library: /usr/local/amber8/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: /usr/local/amber8/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 ions94.lib Loading library: /usr/local/amber8/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: /usr/local/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff eth.lib Loading library: ./eth.lib Loading: eth > loadamberparams frcmod.dummy Loading parameters: ./frcmod.dummy Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: DH) > molecule1 = loadpdb eth2meth.pdb Loading PDB file: ./eth2meth.pdb Matching PDB residue names to LEaP variables. (Residue 0: eth, Terminal/last, was not found in name map.) (Residue 1: WAT, Terminal/last, was not found in name map.) (Residue 2: WAT, Terminal/last, was not found in name map.) (Residue 3: WAT, Terminal/last, was not found in name map.) (Residue 4: WAT, Terminal/last, was not found in name map.) (Residue 5: WAT, Terminal/last, was not found in name map.) (Residue 6: WAT, Terminal/last, was not found in name map.) (Residue 7: WAT, Terminal/last, was not found in name map.) total atoms in file: 29 > edit molecule1 > saveamberparmpert molecule1 eth2meth.prmtop eth2meth.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 0 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 7 eth 1 ) (no restraints) > molecule2 = loadpdb eth2meth.pdb Loading PDB file: ./eth2meth.pdb Matching PDB residue names to LEaP variables. (Residue 0: eth, Terminal/last, was not found in name map.) (Residue 1: WAT, Terminal/last, was not found in name map.) (Residue 2: WAT, Terminal/last, was not found in name map.) (Residue 3: WAT, Terminal/last, was not found in name map.) (Residue 4: WAT, Terminal/last, was not found in name map.) (Residue 5: WAT, Terminal/last, was not found in name map.) (Residue 6: WAT, Terminal/last, was not found in name map.) (Residue 7: WAT, Terminal/last, was not found in name map.) total atoms in file: 29 > edit molecule2 Table Editor: Check table... Table Editor: The table has no errors and 0 warnings. Table Editor: Table has been 'saved' back to the program. > help setbox setBox vdw OR centers [ buffer OR buffer_xyz_list ] The setBox command adds a periodic box to the UNIT, turning it into a periodic system for the simulation programs. It does not add any solvent to the system. The choice of 'vdw' or 'centers' determines whether the box encloses the entire atoms or just the atom centers - use 'centers' if the system has been previously equilibrated as a periodic box. See the solvateBox command for a description of the buffer variable, which extends either type of box by an arbitrary amount. > setbox molecule2 vdw Box dimensions: 11.090600 11.668600 12.018600 > setbox molecule1 vdw Box dimensions: 11.090600 11.668600 12.018600 > saveamberparmpert molecule1 eth2meth.prmtop eth2meth.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 0 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 7 eth 1 ) (no restraints) > saveamberparmpert molecule2 meth2eth.prmtop meth2eth.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 0 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 7 eth 1 ) (no restraints) > quit Quit