log started: Sun Apr 23 10:12:27 2006 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: /usr/local/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) >> >> # >> # Load water and ions >> # >> 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 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # 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_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 all_amino03.lib Loading library: /usr/local/amber8/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 T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL WAT frcmod03 parm99 > loadamberprep vit.prepin Loading Prep file: ./vit.prepin (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: c1) Loaded UNIT: VIT > loadamberparams vit.frcmod Loading parameters: ./vit.frcmod Reading force field mod type file (frcmod) > 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 T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL VIT WAT frcmod03 parm99 > edit VIT > vit=loadpdb vit.pdb Loading PDB file: ./vit.pdb Matching PDB residue names to LEaP variables. (Residue 0: VIT, Terminal/last, was not found in name map.) total atoms in file: 31 > 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 T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL VIT WAT frcmod03 parm99 vit > check VIT Checking 'VIT'.... Checking parameters for unit 'VIT'. Checking for bond parameters. Could not find bond parameter for: cg - c1 Could not find bond parameter for: c1 - c3 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c Could not find bond parameter for: c - o Could not find bond parameter for: c - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - os Could not find bond parameter for: os - c3 Could not find bond parameter for: c3 - c1 Could not find bond parameter for: c3 - c1 Could not find bond parameter for: c1 - cg Could not find bond parameter for: cg - cg Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Checking for angle parameters. Could not find angle parameter: c1 - c3 - os Could not find angle parameter: c1 - c3 - c1 Could not find angle parameter: c1 - c3 - c1 Could not find angle parameter: c2 - c2 - c1 Could not find angle parameter: c2 - c2 - c Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: c2 - c2 - os Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: c2 - c - o Could not find angle parameter: c2 - c - c2 Could not find angle parameter: c - c2 - c2 Could not find angle parameter: o - c - c2 Could not find angle parameter: c2 - c2 - c1 Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: c1 - c2 - c2 Could not find angle parameter: c2 - c2 - os Could not find angle parameter: c1 - c2 - c2 Could not find angle parameter: c2 - os - c3 Could not find angle parameter: os - c3 - c1 Could not find angle parameter: os - c3 - c1 Could not find angle parameter: c1 - c3 - c1 Could not find angle parameter: c1 - cg - cg Could not find angle parameter: c2 - c1 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c1 - c1 Could not find angle parameter: c1 - c1 - c2 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c2 - c1 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c1 - c1 Could not find angle parameter: c1 - c1 - c2 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 There are missing parameters. Unit is OK. > check vit Checking 'vit'.... Checking parameters for unit 'vit'. Checking for bond parameters. Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c1 - c2 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c1 - c2 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c1 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: cg - cg Could not find bond parameter for: c1 - cg Could not find bond parameter for: c3 - c1 Could not find bond parameter for: c3 - c1 Could not find bond parameter for: os - c3 Could not find bond parameter for: c2 - os Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c - o Could not find bond parameter for: c - c2 Could not find bond parameter for: c2 - c1 Could not find bond parameter for: c2 - c Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c2 - c2 Could not find bond parameter for: c1 - c3 Could not find bond parameter for: cg - c1 Checking for angle parameters. Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c1 - c2 Could not find angle parameter: c1 - c1 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c2 - c1 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c1 - c1 - c2 Could not find angle parameter: c1 - c1 - c1 Could not find angle parameter: c1 - c2 - c1 Could not find angle parameter: c2 - c1 - c1 Could not find angle parameter: c1 - cg - cg Could not find angle parameter: c1 - c3 - c1 Could not find angle parameter: os - c3 - c1 Could not find angle parameter: os - c3 - c1 Could not find angle parameter: c2 - os - c3 Could not find angle parameter: c1 - c2 - c2 Could not find angle parameter: c2 - c2 - os Could not find angle parameter: c1 - c2 - c2 Could not find angle parameter: c2 - c2 - c1 Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: o - c - c2 Could not find angle parameter: c - c2 - c2 Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: c2 - c - o Could not find angle parameter: c2 - c - c2 Could not find angle parameter: c2 - c2 - c1 Could not find angle parameter: c2 - c2 - c Could not find angle parameter: c2 - c2 - c2 Could not find angle parameter: c2 - c2 - os Could not find angle parameter: c1 - c3 - os Could not find angle parameter: c1 - c3 - c1 Could not find angle parameter: c1 - c3 - c1 There are missing parameters. Unit is OK. > quit Quit log started: Sun Apr 23 10:16:03 2006 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: /usr/local/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) >> >> # >> # Load water and ions >> # >> 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 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # 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_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 all_amino03.lib Loading library: /usr/local/amber8/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /usr/local/amber8/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber8/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Sun Apr 23 10:16:09 2006 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber8/dat/leap/parm/gaff.dat > > loadamberprep vit.prepinm Could not open file vit.prepinm: not found > loadamberprep vit.prepin Loading Prep file: ./vit.prepin Loaded UNIT: VIT > loadamberparams vit.frcmod Loading parameters: ./vit.frcmod Reading force field mod type file (frcmod) > 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 T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL VIT WAT frcmod03 gaff parm99 > check VIT Checking 'VIT'.... Checking parameters for unit 'VIT'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > edit VIT > quit Quit log started: Sun Apr 23 10:17:47 2006 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: /usr/local/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) >> >> # >> # Load water and ions >> # >> 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 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # 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_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 all_amino03.lib Loading library: /usr/local/amber8/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /usr/local/amber8/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber8/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Sun Apr 23 10:17:54 2006 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber8/dat/leap/parm/gaff.dat > > set default PBradii bondi Using Bondi radii > loadamberprep vit.prepin] Could not open file vit.prepin]: not found > loadamberprep vit.prepin Loading Prep file: ./vit.prepin Loaded UNIT: VIT > loadamberparams vit.frcmod Loading parameters: ./vit.frcmod Reading force field mod type file (frcmod) > kpm=loadpdb kpm-vit.pdb Loading PDB file: ./kpm-vit.pdb Matching PDB residue names to LEaP variables. Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER. (Residue 1: LEU, Nonterminal, was not found in name map.) (Residue 2: LEU, Nonterminal, was not found in name map.) (Residue 3: GLU, Nonterminal, was not found in name map.) (Residue 4: PHE, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: MET, Nonterminal, was not found in name map.) (Residue 8: ILE, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLU, Nonterminal, was not found in name map.) (Residue 11: GLU, Nonterminal, was not found in name map.) (Residue 12: THR, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: LYS, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: ALA, Nonterminal, was not found in name map.) (Residue 17: ILE, Nonterminal, was not found in name map.) (Residue 18: PRO, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: TYR, Nonterminal, was not found in name map.) (Residue 21: SER, Nonterminal, was not found in name map.) (Residue 22: SER, Nonterminal, was not found in name map.) (Residue 23: TYR, Nonterminal, was not found in name map.) (Residue 24: GLY, Nonterminal, was not found in name map.) (Residue 25: CYX, Nonterminal, was not found in name map.) (Residue 26: TYR, Nonterminal, was not found in name map.) (Residue 27: CYX, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: TRP, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: LYS, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: LYS, Nonterminal, was not found in name map.) (Residue 37: ASP, Nonterminal, was not found in name map.) (Residue 38: ALA, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: ASP, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: CYX, Nonterminal, was not found in name map.) (Residue 43: CYX, Nonterminal, was not found in name map.) (Residue 44: PHE, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: HIS, Nonterminal, was not found in name map.) (Residue 47: ASP, Nonterminal, was not found in name map.) (Residue 48: CYX, Nonterminal, was not found in name map.) (Residue 49: CYX, Nonterminal, was not found in name map.) (Residue 50: TYR, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: ASN, Nonterminal, was not found in name map.) (Residue 53: LEU, Nonterminal, was not found in name map.) (Residue 54: PRO, Nonterminal, was not found in name map.) (Residue 55: ASP, Nonterminal, was not found in name map.) (Residue 56: CYX, Nonterminal, was not found in name map.) (Residue 57: ASN, Nonterminal, was not found in name map.) (Residue 58: PRO, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: SER, Nonterminal, was not found in name map.) (Residue 61: ASP, Nonterminal, was not found in name map.) (Residue 62: ARG, Nonterminal, was not found in name map.) (Residue 63: TYR, Nonterminal, was not found in name map.) (Residue 64: LYS, Nonterminal, was not found in name map.) (Residue 65: TYR, Nonterminal, was not found in name map.) (Residue 66: LYS, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: VAL, Nonterminal, was not found in name map.) (Residue 69: ASN, Nonterminal, was not found in name map.) (Residue 70: GLY, Nonterminal, was not found in name map.) (Residue 71: ALA, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: CYX, Nonterminal, was not found in name map.) (Residue 75: GLU, Nonterminal, was not found in name map.) (Residue 76: LYS, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: THR, Nonterminal, was not found in name map.) (Residue 79: SER, Nonterminal, was not found in name map.) (Residue 80: CYX, Nonterminal, was not found in name map.) (Residue 81: GLU, Nonterminal, was not found in name map.) (Residue 82: ASN, Nonterminal, was not found in name map.) (Residue 83: ARG, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: CYX, Nonterminal, was not found in name map.) (Residue 86: GLU, Nonterminal, was not found in name map.) (Residue 87: CYX, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: LYS, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: ALA, Nonterminal, was not found in name map.) (Residue 92: ALA, Nonterminal, was not found in name map.) (Residue 93: ILE, Nonterminal, was not found in name map.) (Residue 94: CYX, Nonterminal, was not found in name map.) (Residue 95: PHE, Nonterminal, was not found in name map.) (Residue 96: ARG, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ASN, Nonterminal, was not found in name map.) (Residue 99: LEU, Nonterminal, was not found in name map.) (Residue 100: ASN, Nonterminal, was not found in name map.) (Residue 101: THR, Nonterminal, was not found in name map.) (Residue 102: TYR, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LYS, Nonterminal, was not found in name map.) (Residue 105: LYS, Nonterminal, was not found in name map.) (Residue 106: TYR, Nonterminal, was not found in name map.) (Residue 107: MET, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: TYR, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: ASP, Nonterminal, was not found in name map.) (Residue 112: PHE, Nonterminal, was not found in name map.) (Residue 113: LEU, Nonterminal, was not found in name map.) (Residue 114: CYX, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLY, Nonterminal, was not found in name map.) (Residue 117: GLU, Nonterminal, was not found in name map.) (Residue 118: LEU, Nonterminal, was not found in name map.) (Residue 119: LYS, Nonterminal, was not found in name map.) Mapped residue CYX, term: Terminal/last, seq. number: 120 to: CCYX. (Residue 121: VIT, Terminal/last, was not found in name map.) Joining NSER - LEU Joining LEU - LEU Joining LEU - GLU Joining GLU - PHE Joining PHE - GLY Joining GLY - LYS Joining LYS - MET Joining MET - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - SER Joining SER - SER Joining SER - TYR Joining TYR - GLY Joining GLY - CYX Joining CYX - TYR Joining TYR - CYX Joining CYX - GLY Joining GLY - TRP Joining TRP - GLY Joining GLY - GLY Joining GLY - LYS Joining LYS - GLY Joining GLY - THR Joining THR - PRO Joining PRO - LYS Joining LYS - ASP Joining ASP - ALA Joining ALA - THR Joining THR - ASP Joining ASP - ARG Joining ARG - CYX Joining CYX - CYX Joining CYX - PHE Joining PHE - VAL Joining VAL - HIE Joining HIE - ASP Joining ASP - CYX Joining CYX - CYX Joining CYX - TYR Joining TYR - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - PRO Joining PRO - ASP Joining ASP - CYX Joining CYX - ASN Joining ASN - PRO Joining PRO - LYS Joining LYS - SER Joining SER - ASP Joining ASP - ARG Joining ARG - TYR Joining TYR - LYS Joining LYS - TYR Joining TYR - LYS Joining LYS - ARG Joining ARG - VAL Joining VAL - ASN Joining ASN - GLY Joining GLY - ALA Joining ALA - ILE Joining ILE - VAL Joining VAL - CYX Joining CYX - GLU Joining GLU - LYS Joining LYS - GLY Joining GLY - THR Joining THR - SER Joining SER - CYX Joining CYX - GLU Joining GLU - ASN Joining ASN - ARG Joining ARG - ILE Joining ILE - CYX Joining CYX - GLU Joining GLU - CYX Joining CYX - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - ILE Joining ILE - CYX Joining CYX - PHE Joining PHE - ARG Joining ARG - GLN Joining GLN - ASN Joining ASN - LEU Joining LEU - ASN Joining ASN - THR Joining THR - TYR Joining TYR - SER Joining SER - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - MET Joining MET - LEU Joining LEU - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - CYX Joining CYX - LYS Joining LYS - GLY Joining GLY - GLU Joining GLU - LEU Joining LEU - LYS Joining LYS - CCYX total atoms in file: 975 Leap added 907 missing atoms according to residue templates: 907 H / lone pairs > check kpm Checking 'kpm'.... WARNING: The unperturbed charge of the unit: 4.000000 is not zero. Warning: Close contact of 1.035289 angstroms between .R.A and .R.A Warning: Close contact of 2.146839 angstroms between .R.A and .R.A Warning: Close contact of 2.234500 angstroms between .R.A and .R.A Warning: Close contact of 1.046580 angstroms between .R.A and .R.A Warning: Close contact of 1.556705 angstroms between .R.A and .R.A Checking parameters for unit 'kpm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 6 Unit is OK. > edit kpm > bond kpm.26.SG kpm.115.SG > bond kpm.28.SG kpm.44.SG > bond kpm.43.SG kpm.95.SG > bond kpm.49.SG kpm.121.SG > bond kpm.50.SG kpm.88.SG > bond kpm.57.SG kpm.81.SG > bond kpm.75.SG kpm.86.SG > savepdv kpm kpm-gb.pdb ERROR: syntax error > savepdb kpm kpm-gb.pdb Writing pdb file: kpm-gb.pdb Shortening residue name for PDB format: NSER -> SER Shortening residue name for PDB format: CCYX -> CYX > saveamberparm kpm kpm-gb.prmtop kpm-gb.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 4.000000 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. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for c1-c1-c2-c1 atoms are: C26 C29 C27 C28 ** Warning: No sp2 improper torsion term for c1-c1-c2-c1 atoms are: C22 C1 C23 C24 ** Warning: No sp2 improper torsion term for cg-c1-c2-c1 atoms are: C17 C19 C18 C20 ** Warning: No sp2 improper torsion term for c2-os-c2-c2 atoms are: C5 O1 C4 C3 ** Warning: No sp2 improper torsion term for c2-c1-c2-c2 atoms are: C6 C12 C5 C4 ** Warning: No sp2 improper torsion term for c-c1-c2-c2 atoms are: C7 C13 C6 C5 ** Warning: No sp2 improper torsion term for c2-c1-c2-c atoms are: C3 C8 C2 C7 ** Warning: No sp2 improper torsion term for cg-c2-c2-c2 atoms are: C10 C2 C3 C4 old PREP-specified impropers: : C4 C2 C3 C10 : C8 C3 C2 C7 : C6 C2 C7 O2 : C13 C5 C6 C7 : C12 C6 C5 C4 : C5 C3 C4 O1 : C19 C20 C18 C17 : C22 C1 C23 C24 : C26 C29 C27 C28 total 379 improper torsions applied 9 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CCYX 1 NSER 1 ) (no restraints) > quit Quit