log started: Thu Jun 25 06:55:50 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the Cornell et al. topology and >> # parm96.dat for proteins >> # 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. >> # >> parm96 = loadamberparams parm96.dat Loading parameters: /Users/jchodera/local/src/amber10/dat/leap/parm/parm96.dat Reading title: PARM96 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs (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) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_amino94.lib Loading library: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff all_aminont94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> loadOff ions94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> >> # >> # 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 > > > # Load GAFF parameters. > source leaprc.gaff ----- Source: /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.gaff ----- Source of /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Thu Jun 25 06:55:50 2009 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /Users/jchodera/local/src/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > > # Set GB radii to recommended values for OBC. > set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > # Load in protein. > receptor = loadPdb receptor.pdb Loading PDB file: ./receptor.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: ASN, Nonterminal, was not found in name map.) (Residue 2: ILE, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: MET, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: ARG, Nonterminal, was not found in name map.) (Residue 8: ILE, Nonterminal, was not found in name map.) (Residue 9: ASP, Nonterminal, was not found in name map.) (Residue 10: GLU, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: ARG, Nonterminal, was not found in name map.) (Residue 14: LEU, Nonterminal, was not found in name map.) (Residue 15: LYS, Nonterminal, was not found in name map.) (Residue 16: ILE, Nonterminal, was not found in name map.) (Residue 17: TYR, Nonterminal, was not found in name map.) (Residue 18: LYS, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: GLU, Nonterminal, was not found in name map.) (Residue 22: GLY, Nonterminal, was not found in name map.) (Residue 23: TYR, Nonterminal, was not found in name map.) (Residue 24: TYR, Nonterminal, was not found in name map.) (Residue 25: THR, Nonterminal, was not found in name map.) (Residue 26: ILE, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: ILE, Nonterminal, was not found in name map.) (Residue 29: GLY, Nonterminal, was not found in name map.) (Residue 30: HIE, Nonterminal, was not found in name map.) (Residue 31: LEU, Nonterminal, was not found in name map.) (Residue 32: LEU, Nonterminal, was not found in name map.) (Residue 33: THR, Nonterminal, was not found in name map.) (Residue 34: LYS, Nonterminal, was not found in name map.) (Residue 35: SER, Nonterminal, was not found in name map.) (Residue 36: PRO, Nonterminal, was not found in name map.) (Residue 37: SER, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: ASN, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: ALA, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLU, Nonterminal, was not found in name map.) (Residue 45: LEU, Nonterminal, was not found in name map.) (Residue 46: ASP, Nonterminal, was not found in name map.) (Residue 47: LYS, Nonterminal, was not found in name map.) (Residue 48: ALA, Nonterminal, was not found in name map.) (Residue 49: ILE, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: ARG, Nonterminal, was not found in name map.) (Residue 52: ASN, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: GLY, Nonterminal, was not found in name map.) (Residue 56: VAL, Nonterminal, was not found in name map.) (Residue 57: ILE, Nonterminal, was not found in name map.) (Residue 58: THR, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: ALA, Nonterminal, was not found in name map.) (Residue 63: GLU, Nonterminal, was not found in name map.) (Residue 64: LYS, Nonterminal, was not found in name map.) (Residue 65: LEU, Nonterminal, was not found in name map.) (Residue 66: PHE, Nonterminal, was not found in name map.) (Residue 67: ASN, Nonterminal, was not found in name map.) (Residue 68: GLN, Nonterminal, was not found in name map.) (Residue 69: ASP, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: ASP, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: ALA, Nonterminal, was not found in name map.) (Residue 74: VAL, Nonterminal, was not found in name map.) (Residue 75: ARG, Nonterminal, was not found in name map.) (Residue 76: GLY, Nonterminal, was not found in name map.) (Residue 77: ILE, Nonterminal, was not found in name map.) (Residue 78: LEU, Nonterminal, was not found in name map.) (Residue 79: ARG, Nonterminal, was not found in name map.) (Residue 80: ASN, Nonterminal, was not found in name map.) (Residue 81: ALA, Nonterminal, was not found in name map.) (Residue 82: LYS, Nonterminal, was not found in name map.) (Residue 83: LEU, Nonterminal, was not found in name map.) (Residue 84: LYS, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) (Residue 86: VAL, Nonterminal, was not found in name map.) (Residue 87: TYR, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: SER, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: ASP, Nonterminal, was not found in name map.) (Residue 92: ALA, Nonterminal, was not found in name map.) (Residue 93: VAL, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: ALA, Nonterminal, was not found in name map.) (Residue 97: ALA, Nonterminal, was not found in name map.) (Residue 98: ALA, Nonterminal, was not found in name map.) (Residue 99: ILE, Nonterminal, was not found in name map.) (Residue 100: ASN, Nonterminal, was not found in name map.) (Residue 101: MET, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: PHE, Nonterminal, was not found in name map.) (Residue 104: GLN, Nonterminal, was not found in name map.) (Residue 105: MET, Nonterminal, was not found in name map.) (Residue 106: GLY, Nonterminal, was not found in name map.) (Residue 107: GLU, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: VAL, Nonterminal, was not found in name map.) (Residue 111: ALA, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: PHE, Nonterminal, was not found in name map.) (Residue 114: THR, Nonterminal, was not found in name map.) (Residue 115: ASN, Nonterminal, was not found in name map.) (Residue 116: SER, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ARG, Nonterminal, was not found in name map.) (Residue 119: MET, Nonterminal, was not found in name map.) (Residue 120: LEU, Nonterminal, was not found in name map.) (Residue 121: GLN, Nonterminal, was not found in name map.) (Residue 122: GLN, Nonterminal, was not found in name map.) (Residue 123: LYS, Nonterminal, was not found in name map.) (Residue 124: ARG, Nonterminal, was not found in name map.) (Residue 125: TRP, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: VAL, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ALA, Nonterminal, was not found in name map.) (Residue 134: LYS, Nonterminal, was not found in name map.) (Residue 135: SER, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: TRP, Nonterminal, was not found in name map.) (Residue 138: TYR, Nonterminal, was not found in name map.) (Residue 139: ASN, Nonterminal, was not found in name map.) (Residue 140: GLN, Nonterminal, was not found in name map.) (Residue 141: THR, Nonterminal, was not found in name map.) (Residue 142: PRO, Nonterminal, was not found in name map.) (Residue 143: ASN, Nonterminal, was not found in name map.) (Residue 144: ARG, Nonterminal, was not found in name map.) (Residue 145: ALA, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ARG, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: ILE, Nonterminal, was not found in name map.) (Residue 150: THR, Nonterminal, was not found in name map.) (Residue 151: THR, Nonterminal, was not found in name map.) (Residue 152: PHE, Nonterminal, was not found in name map.) (Residue 153: ARG, Nonterminal, was not found in name map.) (Residue 154: THR, Nonterminal, was not found in name map.) (Residue 155: GLY, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: TRP, Nonterminal, was not found in name map.) (Residue 158: ASP, Nonterminal, was not found in name map.) (Residue 159: ALA, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 161 to: CLYS. Joining NMET - ASN Joining ASN - ILE Joining ILE - PHE Joining PHE - GLU Joining GLU - MET Joining MET - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - ASP Joining ASP - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LYS Joining LYS - ILE Joining ILE - TYR Joining TYR - LYS Joining LYS - ASP Joining ASP - THR Joining THR - GLU Joining GLU - GLY Joining GLY - TYR Joining TYR - TYR Joining TYR - THR Joining THR - ILE Joining ILE - GLY Joining GLY - ILE Joining ILE - GLY Joining GLY - HIE Joining HIE - LEU Joining LEU - LEU Joining LEU - THR Joining THR - LYS Joining LYS - SER Joining SER - PRO Joining PRO - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - LYS Joining LYS - SER Joining SER - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - ILE Joining ILE - GLY Joining GLY - ARG Joining ARG - ASN Joining ASN - THR Joining THR - ASN Joining ASN - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - THR Joining THR - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - LYS Joining LYS - LEU Joining LEU - PHE Joining PHE - ASN Joining ASN - GLN Joining GLN - ASP Joining ASP - VAL Joining VAL - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - TYR Joining TYR - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - ILE Joining ILE - ASN Joining ASN - MET Joining MET - VAL Joining VAL - PHE Joining PHE - GLN Joining GLN - MET Joining MET - GLY Joining GLY - GLU Joining GLU - THR Joining THR - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - PHE Joining PHE - THR Joining THR - ASN Joining ASN - SER Joining SER - LEU Joining LEU - ARG Joining ARG - MET Joining MET - LEU Joining LEU - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - ARG Joining ARG - TRP Joining TRP - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ASN Joining ASN - LEU Joining LEU - ALA Joining ALA - LYS Joining LYS - SER Joining SER - ARG Joining ARG - TRP Joining TRP - TYR Joining TYR - ASN Joining ASN - GLN Joining GLN - THR Joining THR - PRO Joining PRO - ASN Joining ASN - ARG Joining ARG - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - VAL Joining VAL - ILE Joining ILE - THR Joining THR - THR Joining THR - PHE Joining PHE - ARG Joining ARG - THR Joining THR - GLY Joining GLY - THR Joining THR - TRP Joining TRP - ASP Joining ASP - ALA Joining ALA - TYR Joining TYR - CLYS total atoms in file: 1290 Leap added 1313 missing atoms according to residue templates: 1313 H / lone pairs > > # Load parameters for ligand. > mods = loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > > # Load parameters for ligand. > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > > # Load ligand. > ligand = loadMol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named TMP > > # Create complex. > complex = combine { receptor ligand } Sequence: Sequence: TMP > > # Check complex. > check complex Checking 'complex'.... WARNING: The unperturbed charge of the unit: 8.000200 is not zero. Warning: Close contact of 1.518782 angstroms between .R.A and .R.A Warning: Close contact of 2.072268 angstroms between .R.A and .R.A Checking parameters for unit 'complex'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > # Report on net charge. > charge complex Total unperturbed charge: 8.000200 Total perturbed charge: 8.000200 > > # Write parameters. > saveAmberParm ligand ligand.prmtop ligand.crd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 6 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 TMP 1 ) (no restraints) > saveAmberParm receptor receptor.prmtop receptor.crd Checking Unit. WARNING: The unperturbed charge of the unit: 8.000000 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 C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 516 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 CLYS 1 NMET 1 ) (no restraints) > saveAmberParm complex complex.prmtop complex.crd Checking Unit. WARNING: The unperturbed charge of the unit: 8.000200 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 NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 total 522 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 CLYS 1 NMET 1 TMP 1 ) (no restraints) > > # Exit > quit Quit