log started: Wed Mar 3 18:55:14 2004 Log file: ./leap.log >> # >> # ----- leaprc for loading the 2002 pol. 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" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /redfish/people/sbrozell/amber/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_nucleic02.lib Loading library: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/all_nucleic02.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_amino02.lib Loading library: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/all_amino02.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_aminoct02.lib Loading library: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/all_aminoct02.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: NME >> loadOff all_aminont02.lib Loading library: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/all_aminont02.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: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: TIP3PBOX Loading: TIP4PBOX 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 >> > > bpti=loadpdb 6pti.mod.pdb Loading PDB file: ./6pti.mod.pdb Matching PDB residue names to LEaP variables. Mapped residue ARG, term: Terminal/beginning, seq. number: 0 to: NARG. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: ASP, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: CYX, Nonterminal, was not found in name map.) (Residue 5: LEU, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: TYR, Nonterminal, was not found in name map.) (Residue 10: THR, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: CYX, Nonterminal, was not found in name map.) (Residue 14: LYS, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: ILE, Nonterminal, was not found in name map.) (Residue 18: ILE, Nonterminal, was not found in name map.) (Residue 19: ARG, Nonterminal, was not found in name map.) (Residue 20: TYR, Nonterminal, was not found in name map.) (Residue 21: PHE, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: ASN, Nonterminal, was not found in name map.) (Residue 24: ALA, Nonterminal, was not found in name map.) (Residue 25: LYS, Nonterminal, was not found in name map.) (Residue 26: ALA, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: CYX, Nonterminal, was not found in name map.) (Residue 30: GLN, Nonterminal, was not found in name map.) (Residue 31: THR, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: GLY, Nonterminal, was not found in name map.) (Residue 37: CYX, Nonterminal, was not found in name map.) (Residue 38: ARG, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: LYS, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: ASN, Nonterminal, was not found in name map.) (Residue 43: ASN, Nonterminal, was not found in name map.) (Residue 44: PHE, Nonterminal, was not found in name map.) (Residue 45: LYS, Nonterminal, was not found in name map.) (Residue 46: SER, Nonterminal, was not found in name map.) (Residue 47: ALA, Nonterminal, was not found in name map.) (Residue 48: GLU, Nonterminal, was not found in name map.) (Residue 49: ASP, Nonterminal, was not found in name map.) (Residue 50: CYX, Nonterminal, was not found in name map.) (Residue 51: MET, Nonterminal, was not found in name map.) (Residue 52: ARG, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: CYX, Nonterminal, was not found in name map.) (Residue 55: GLY, Nonterminal, was not found in name map.) Mapped residue GLY, term: Terminal/last, seq. number: 56 to: CGLY. Joining NARG - PRO Joining PRO - ASP Joining ASP - PHE Joining PHE - CYX Joining CYX - LEU Joining LEU - GLU Joining GLU - PRO Joining PRO - PRO Joining PRO - TYR Joining TYR - THR Joining THR - GLY Joining GLY - PRO Joining PRO - CYX Joining CYX - LYS Joining LYS - ALA Joining ALA - ARG Joining ARG - ILE Joining ILE - ILE Joining ILE - ARG Joining ARG - TYR Joining TYR - PHE Joining PHE - TYR Joining TYR - ASN Joining ASN - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - GLY Joining GLY - LEU Joining LEU - CYX Joining CYX - GLN Joining GLN - THR Joining THR - PHE Joining PHE - VAL Joining VAL - TYR Joining TYR - GLY Joining GLY - GLY Joining GLY - CYX Joining CYX - ARG Joining ARG - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - ASN Joining ASN - ASN Joining ASN - PHE Joining PHE - LYS Joining LYS - SER Joining SER - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - CYX Joining CYX - MET Joining MET - ARG Joining ARG - THR Joining THR - CYX Joining CYX - GLY Joining GLY - CGLY Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 445 Leap added 437 missing atoms according to residue templates: 4 Heavy 433 H / lone pairs > quit Quit log started: Wed Mar 3 18:56:19 2004 Log file: ./leap.log >> # >> # ----- leaprc for loading the Cornell et al. 1994 force field. >> # 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" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm94 = loadamberparams parm94.dat Loading parameters: /redfish/people/sbrozell/amber/amber8/dat/leap/parm/parm94.dat (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: IB) (UNKNOWN ATOM TYPE: EP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/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: /redfish/people/sbrozell/amber/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: TIP3PBOX Loading: TIP4PBOX 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 > > bpti = loadPdb 6pti.mod.pdb Loading PDB file: ./6pti.mod.pdb Matching PDB residue names to LEaP variables. Mapped residue ARG, term: Terminal/beginning, seq. number: 0 to: NARG. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: ASP, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: CYX, Nonterminal, was not found in name map.) (Residue 5: LEU, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: TYR, Nonterminal, was not found in name map.) (Residue 10: THR, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: CYX, Nonterminal, was not found in name map.) (Residue 14: LYS, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: ILE, Nonterminal, was not found in name map.) (Residue 18: ILE, Nonterminal, was not found in name map.) (Residue 19: ARG, Nonterminal, was not found in name map.) (Residue 20: TYR, Nonterminal, was not found in name map.) (Residue 21: PHE, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: ASN, Nonterminal, was not found in name map.) (Residue 24: ALA, Nonterminal, was not found in name map.) (Residue 25: LYS, Nonterminal, was not found in name map.) (Residue 26: ALA, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: CYX, Nonterminal, was not found in name map.) (Residue 30: GLN, Nonterminal, was not found in name map.) (Residue 31: THR, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: GLY, Nonterminal, was not found in name map.) (Residue 37: CYX, Nonterminal, was not found in name map.) (Residue 38: ARG, Nonterminal, was not found in name map.) (Residue 39: ALA, Nonterminal, was not found in name map.) (Residue 40: LYS, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: ASN, Nonterminal, was not found in name map.) (Residue 43: ASN, Nonterminal, was not found in name map.) (Residue 44: PHE, Nonterminal, was not found in name map.) (Residue 45: LYS, Nonterminal, was not found in name map.) (Residue 46: SER, Nonterminal, was not found in name map.) (Residue 47: ALA, Nonterminal, was not found in name map.) (Residue 48: GLU, Nonterminal, was not found in name map.) (Residue 49: ASP, Nonterminal, was not found in name map.) (Residue 50: CYX, Nonterminal, was not found in name map.) (Residue 51: MET, Nonterminal, was not found in name map.) (Residue 52: ARG, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: CYX, Nonterminal, was not found in name map.) (Residue 55: GLY, Nonterminal, was not found in name map.) Mapped residue GLY, term: Terminal/last, seq. number: 56 to: CGLY. Joining NARG - PRO Joining PRO - ASP Joining ASP - PHE Joining PHE - CYX Joining CYX - LEU Joining LEU - GLU Joining GLU - PRO Joining PRO - PRO Joining PRO - TYR Joining TYR - THR Joining THR - GLY Joining GLY - PRO Joining PRO - CYX Joining CYX - LYS Joining LYS - ALA Joining ALA - ARG Joining ARG - ILE Joining ILE - ILE Joining ILE - ARG Joining ARG - TYR Joining TYR - PHE Joining PHE - TYR Joining TYR - ASN Joining ASN - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - GLY Joining GLY - LEU Joining LEU - CYX Joining CYX - GLN Joining GLN - THR Joining THR - PHE Joining PHE - VAL Joining VAL - TYR Joining TYR - GLY Joining GLY - GLY Joining GLY - CYX Joining CYX - ARG Joining ARG - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - ASN Joining ASN - ASN Joining ASN - PHE Joining PHE - LYS Joining LYS - SER Joining SER - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - CYX Joining CYX - MET Joining MET - ARG Joining ARG - THR Joining THR - CYX Joining CYX - GLY Joining GLY - CGLY Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 445 Leap added 437 missing atoms according to residue templates: 4 Heavy 433 H / lone pairs > bond bpti.5.SG bpti.55.SG > bond bpti.14.SG bpti.38.SG > bond bpti.30.SG bpti.51.SG > saveAmberParm bpti bpti.prmtop prmcrd Checking Unit. WARNING: The unperturbed charge of the unit: 6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 197 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 CGLY 1 NARG 1 ) (no restraints) > savepdb bpti bpti.pdb Writing pdb file: bpti.pdb Shortening residue name for PDB format: NARG -> ARG Shortening residue name for PDB format: CGLY -> GLY