log started: Sat Jun 23 09:02:25 2012 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # modified for the "ILDN" changes >> # >> # 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" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> #ildn >> { "C3" "C" "sp3" } >> { "C4" "C" "sp3" } >> { "C5" "C" "sp2" } >> { "C6" "C" "sp2" } >> { "NP" "N" "sp2" } >> { "OM" "O" "sp2" } # guess!!! >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: 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) >> mods = loadamberparams frcmod.ff99SBildn Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.ff99SBildn Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) + ILDN corrections >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /Users/jchodera.mobile/local/src/amber11/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 (i.e. ff94 libs) >> # >> loadOff all_amino94ildn.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_amino94ildn.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_aminoct94ildn.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_aminoct94ildn.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_aminont94ildn.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_aminont94ildn.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 >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /Users/jchodera.mobile/local/src/amber11/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.mobile/local/src/amber11/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" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "O2*" "O2'" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > > # Load GAFF parameters for ligand. > source leaprc.gaff ----- Source: /Users/jchodera.mobile/local/src/amber11/dat/leap/cmd/leaprc.gaff ----- Source of /Users/jchodera.mobile/local/src/amber11/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Sat Jun 23 09:02:26 2012 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.mobile/local/src/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > > # Load in protein (with all residues modeled in). > receptor = loadPdb ../../modeller/output.pdb Loading PDB file: ../../modeller/output.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY. (Residue 1: HIS, Nonterminal, was not found in name map.) (Residue 2: MET, Nonterminal, was not found in name map.) (Residue 3: GLN, Nonterminal, was not found in name map.) (Residue 4: THR, Nonterminal, was not found in name map.) (Residue 5: GLN, Nonterminal, was not found in name map.) (Residue 6: GLY, Nonterminal, was not found in name map.) (Residue 7: LEU, Nonterminal, was not found in name map.) (Residue 8: ALA, Nonterminal, was not found in name map.) (Residue 9: LYS, Nonterminal, was not found in name map.) (Residue 10: ASP, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: TRP, Nonterminal, was not found in name map.) (Residue 13: GLU, Nonterminal, was not found in name map.) (Residue 14: ILE, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: GLU, Nonterminal, was not found in name map.) (Residue 18: SER, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: GLU, Nonterminal, was not found in name map.) (Residue 23: VAL, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: LEU, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLN, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: CYS, Nonterminal, was not found in name map.) (Residue 30: PHE, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: TRP, Nonterminal, was not found in name map.) (Residue 35: MET, Nonterminal, was not found in name map.) (Residue 36: GLY, Nonterminal, was not found in name map.) (Residue 37: THR, Nonterminal, was not found in name map.) (Residue 38: TRP, Nonterminal, was not found in name map.) (Residue 39: ASN, Nonterminal, was not found in name map.) (Residue 40: GLY, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: ARG, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: ALA, Nonterminal, was not found in name map.) (Residue 46: ILE, Nonterminal, was not found in name map.) (Residue 47: LYS, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: LEU, Nonterminal, was not found in name map.) (Residue 50: LYS, Nonterminal, was not found in name map.) (Residue 51: PRO, Nonterminal, was not found in name map.) (Residue 52: GLY, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: MET, Nonterminal, was not found in name map.) (Residue 55: SER, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) (Residue 57: GLU, Nonterminal, was not found in name map.) (Residue 58: ALA, Nonterminal, was not found in name map.) (Residue 59: PHE, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: GLN, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ALA, Nonterminal, was not found in name map.) (Residue 64: GLN, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: MET, Nonterminal, was not found in name map.) (Residue 67: LYS, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: LEU, Nonterminal, was not found in name map.) (Residue 70: ARG, Nonterminal, was not found in name map.) (Residue 71: HIS, Nonterminal, was not found in name map.) (Residue 72: GLU, Nonterminal, was not found in name map.) (Residue 73: LYS, Nonterminal, was not found in name map.) (Residue 74: LEU, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: GLN, Nonterminal, was not found in name map.) (Residue 77: LEU, Nonterminal, was not found in name map.) (Residue 78: TYR, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: VAL, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLU, Nonterminal, was not found in name map.) (Residue 84: GLU, Nonterminal, was not found in name map.) (Residue 85: PRO, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: TYR, Nonterminal, was not found in name map.) (Residue 88: ILE, Nonterminal, was not found in name map.) (Residue 89: VAL, Nonterminal, was not found in name map.) (Residue 90: THR, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: TYR, Nonterminal, was not found in name map.) (Residue 93: MET, Nonterminal, was not found in name map.) (Residue 94: SER, Nonterminal, was not found in name map.) (Residue 95: LYS, Nonterminal, was not found in name map.) (Residue 96: GLY, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: LEU, Nonterminal, was not found in name map.) (Residue 99: LEU, Nonterminal, was not found in name map.) (Residue 100: ASP, Nonterminal, was not found in name map.) (Residue 101: PHE, Nonterminal, was not found in name map.) (Residue 102: LEU, Nonterminal, was not found in name map.) (Residue 103: LYS, Nonterminal, was not found in name map.) (Residue 104: GLY, Nonterminal, was not found in name map.) (Residue 105: GLU, Nonterminal, was not found in name map.) (Residue 106: MET, Nonterminal, was not found in name map.) (Residue 107: GLY, Nonterminal, was not found in name map.) (Residue 108: LYS, Nonterminal, was not found in name map.) (Residue 109: TYR, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: ARG, Nonterminal, was not found in name map.) (Residue 112: LEU, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: GLN, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: VAL, Nonterminal, was not found in name map.) (Residue 117: ASP, Nonterminal, was not found in name map.) (Residue 118: MET, Nonterminal, was not found in name map.) (Residue 119: ALA, Nonterminal, was not found in name map.) (Residue 120: ALA, Nonterminal, was not found in name map.) (Residue 121: GLN, Nonterminal, was not found in name map.) (Residue 122: ILE, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: SER, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: MET, Nonterminal, was not found in name map.) (Residue 127: ALA, Nonterminal, was not found in name map.) (Residue 128: TYR, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: GLU, Nonterminal, was not found in name map.) (Residue 131: ARG, Nonterminal, was not found in name map.) (Residue 132: MET, Nonterminal, was not found in name map.) (Residue 133: ASN, Nonterminal, was not found in name map.) (Residue 134: TYR, Nonterminal, was not found in name map.) (Residue 135: VAL, Nonterminal, was not found in name map.) (Residue 136: HIS, Nonterminal, was not found in name map.) (Residue 137: ARG, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: LEU, Nonterminal, was not found in name map.) (Residue 140: ARG, Nonterminal, was not found in name map.) (Residue 141: ALA, Nonterminal, was not found in name map.) (Residue 142: ALA, Nonterminal, was not found in name map.) (Residue 143: ASN, Nonterminal, was not found in name map.) (Residue 144: ILE, Nonterminal, was not found in name map.) (Residue 145: LEU, Nonterminal, was not found in name map.) (Residue 146: VAL, Nonterminal, was not found in name map.) (Residue 147: GLY, Nonterminal, was not found in name map.) (Residue 148: GLU, Nonterminal, was not found in name map.) (Residue 149: ASN, Nonterminal, was not found in name map.) (Residue 150: LEU, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: CYS, Nonterminal, was not found in name map.) (Residue 153: LYS, Nonterminal, was not found in name map.) (Residue 154: VAL, Nonterminal, was not found in name map.) (Residue 155: ALA, Nonterminal, was not found in name map.) (Residue 156: ASP, Nonterminal, was not found in name map.) (Residue 157: PHE, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: LEU, Nonterminal, was not found in name map.) (Residue 160: ALA, Nonterminal, was not found in name map.) (Residue 161: ARG, Nonterminal, was not found in name map.) (Residue 162: LEU, Nonterminal, was not found in name map.) (Residue 163: ILE, Nonterminal, was not found in name map.) (Residue 164: GLU, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: ASN, Nonterminal, was not found in name map.) (Residue 167: GLU, Nonterminal, was not found in name map.) (Residue 168: TYR, Nonterminal, was not found in name map.) (Residue 169: THR, Nonterminal, was not found in name map.) (Residue 170: ALA, Nonterminal, was not found in name map.) (Residue 171: ARG, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: GLY, Nonterminal, was not found in name map.) (Residue 174: ALA, Nonterminal, was not found in name map.) (Residue 175: LYS, Nonterminal, was not found in name map.) (Residue 176: PHE, Nonterminal, was not found in name map.) (Residue 177: PRO, Nonterminal, was not found in name map.) (Residue 178: ILE, Nonterminal, was not found in name map.) (Residue 179: LYS, Nonterminal, was not found in name map.) (Residue 180: TRP, Nonterminal, was not found in name map.) (Residue 181: THR, Nonterminal, was not found in name map.) (Residue 182: ALA, Nonterminal, was not found in name map.) (Residue 183: PRO, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) (Residue 185: ALA, Nonterminal, was not found in name map.) (Residue 186: ALA, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: TYR, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ARG, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: THR, Nonterminal, was not found in name map.) (Residue 193: ILE, Nonterminal, was not found in name map.) (Residue 194: LYS, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: TRP, Nonterminal, was not found in name map.) (Residue 199: SER, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: GLY, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: LEU, Nonterminal, was not found in name map.) (Residue 204: LEU, Nonterminal, was not found in name map.) (Residue 205: THR, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: THR, Nonterminal, was not found in name map.) (Residue 210: LYS, Nonterminal, was not found in name map.) (Residue 211: GLY, Nonterminal, was not found in name map.) (Residue 212: ARG, Nonterminal, was not found in name map.) (Residue 213: VAL, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: TYR, Nonterminal, was not found in name map.) (Residue 216: PRO, Nonterminal, was not found in name map.) (Residue 217: GLY, Nonterminal, was not found in name map.) (Residue 218: MET, Nonterminal, was not found in name map.) (Residue 219: VAL, Nonterminal, was not found in name map.) (Residue 220: ASN, Nonterminal, was not found in name map.) (Residue 221: ARG, Nonterminal, was not found in name map.) (Residue 222: GLU, Nonterminal, was not found in name map.) (Residue 223: VAL, Nonterminal, was not found in name map.) (Residue 224: LEU, Nonterminal, was not found in name map.) (Residue 225: ASP, Nonterminal, was not found in name map.) (Residue 226: GLN, Nonterminal, was not found in name map.) (Residue 227: VAL, Nonterminal, was not found in name map.) (Residue 228: GLU, Nonterminal, was not found in name map.) (Residue 229: ARG, Nonterminal, was not found in name map.) (Residue 230: GLY, Nonterminal, was not found in name map.) (Residue 231: TYR, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: MET, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: CYS, Nonterminal, was not found in name map.) (Residue 236: PRO, Nonterminal, was not found in name map.) (Residue 237: PRO, Nonterminal, was not found in name map.) (Residue 238: GLU, Nonterminal, was not found in name map.) (Residue 239: CYS, Nonterminal, was not found in name map.) (Residue 240: PRO, Nonterminal, was not found in name map.) (Residue 241: GLU, Nonterminal, was not found in name map.) (Residue 242: SER, Nonterminal, was not found in name map.) (Residue 243: LEU, Nonterminal, was not found in name map.) (Residue 244: HIS, Nonterminal, was not found in name map.) (Residue 245: ASP, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: CYS, Nonterminal, was not found in name map.) (Residue 249: GLN, Nonterminal, was not found in name map.) (Residue 250: CYS, Nonterminal, was not found in name map.) (Residue 251: TRP, Nonterminal, was not found in name map.) (Residue 252: ARG, Nonterminal, was not found in name map.) (Residue 253: LYS, Nonterminal, was not found in name map.) (Residue 254: ASP, Nonterminal, was not found in name map.) (Residue 255: PRO, Nonterminal, was not found in name map.) (Residue 256: GLU, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: ARG, Nonterminal, was not found in name map.) (Residue 259: PRO, Nonterminal, was not found in name map.) (Residue 260: THR, Nonterminal, was not found in name map.) (Residue 261: PHE, Nonterminal, was not found in name map.) (Residue 262: GLU, Nonterminal, was not found in name map.) (Residue 263: TYR, Nonterminal, was not found in name map.) (Residue 264: LEU, Nonterminal, was not found in name map.) (Residue 265: GLN, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: PHE, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: GLU, Nonterminal, was not found in name map.) (Residue 270: ASP, Nonterminal, was not found in name map.) (Residue 271: TYR, Nonterminal, was not found in name map.) (Residue 272: PHE, Nonterminal, was not found in name map.) (Residue 273: THR, Nonterminal, was not found in name map.) (Residue 274: SER, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: GLU, Nonterminal, was not found in name map.) (Residue 277: PRO, Nonterminal, was not found in name map.) (Residue 278: GLN, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLN, Nonterminal, was not found in name map.) (Residue 281: PRO, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: GLU, Nonterminal, was not found in name map.) (Residue 284: ASN, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 285 to: CLEU. Joining NGLY - HIE Joining HIE - MET Joining MET - GLN Joining GLN - THR Joining THR - GLN Joining GLN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - LYS Joining LYS - ASP Joining ASP - ALA Joining ALA - TRP Joining TRP - GLU Joining GLU - ILE Joining ILE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - GLN Joining GLN - GLY Joining GLY - CYS Joining CYS - PHE Joining PHE - GLY Joining GLY - GLU Joining GLU - VAL Joining VAL - TRP Joining TRP - MET Joining MET - GLY Joining GLY - THR Joining THR - TRP Joining TRP - ASN Joining ASN - GLY Joining GLY - THR Joining THR - THR Joining THR - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - ILE Joining ILE - LYS Joining LYS - THR Joining THR - LEU Joining LEU - LYS Joining LYS - PRO Joining PRO - GLY Joining GLY - THR Joining THR - MET Joining MET - SER Joining SER - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - MET Joining MET - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - ARG Joining ARG - HIE Joining HIE - GLU Joining GLU - LYS Joining LYS - LEU Joining LEU - VAL Joining VAL - GLN Joining GLN - LEU Joining LEU - TYR Joining TYR - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - SER Joining SER - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - ILE Joining ILE - TYR Joining TYR - ILE Joining ILE - VAL Joining VAL - THR Joining THR - GLU Joining GLU - TYR Joining TYR - MET Joining MET - SER Joining SER - LYS Joining LYS - GLY Joining GLY - SER Joining SER - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - LYS Joining LYS - GLY Joining GLY - GLU Joining GLU - MET Joining MET - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PRO Joining PRO - GLN Joining GLN - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - MET Joining MET - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - ILE Joining ILE - ALA Joining ALA - SER Joining SER - GLY Joining GLY - MET Joining MET - ALA Joining ALA - TYR Joining TYR - VAL Joining VAL - GLU Joining GLU - ARG Joining ARG - MET Joining MET - ASN Joining ASN - TYR Joining TYR - VAL Joining VAL - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - ARG Joining ARG - ALA Joining ALA - ALA Joining ALA - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - GLU Joining GLU - TYR Joining TYR - THR Joining THR - ALA Joining ALA - ARG Joining ARG - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - LYS Joining LYS - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - LYS Joining LYS - TRP Joining TRP - THR Joining THR - ALA Joining ALA - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - GLY Joining GLY - ARG Joining ARG - PHE Joining PHE - THR Joining THR - ILE Joining ILE - LYS Joining LYS - SER Joining SER - ASP Joining ASP - VAL Joining VAL - TRP Joining TRP - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - LEU Joining LEU - THR Joining THR - THR Joining THR - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - MET Joining MET - VAL Joining VAL - ASN Joining ASN - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASP Joining ASP - GLN Joining GLN - VAL Joining VAL - GLU Joining GLU - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - ARG Joining ARG - MET Joining MET - PRO Joining PRO - CYS Joining CYS - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - CYS Joining CYS - PRO Joining PRO - GLU Joining GLU - SER Joining SER - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - LEU Joining LEU - MET Joining MET - CYS Joining CYS - GLN Joining GLN - CYS Joining CYS - TRP Joining TRP - ARG Joining ARG - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - PRO Joining PRO - THR Joining THR - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - TYR Joining TYR - PHE Joining PHE - THR Joining THR - SER Joining SER - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLN Joining GLN - TYR Joining TYR - GLN Joining GLN - PRO Joining PRO - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - CLEU total atoms in file: 2295 Leap added 2279 missing atoms according to residue templates: 2279 H / lone pairs > > # Load crystal waters near this copy. > closewaters = loadPdb ../../modeller/closewater.pdb Loading PDB file: ../../modeller/closewater.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: HOH, Terminal/beginning, was not found in name map.) (Residue 1: HOH, Nonterminal, was not found in name map.) (Residue 2: HOH, Nonterminal, was not found in name map.) (Residue 3: HOH, Nonterminal, was not found in name map.) (Residue 4: HOH, Nonterminal, was not found in name map.) (Residue 5: HOH, Nonterminal, was not found in name map.) (Residue 6: HOH, Nonterminal, was not found in name map.) (Residue 7: HOH, Nonterminal, was not found in name map.) (Residue 8: HOH, Nonterminal, was not found in name map.) (Residue 9: HOH, Nonterminal, was not found in name map.) (Residue 10: HOH, Nonterminal, was not found in name map.) (Residue 11: HOH, Nonterminal, was not found in name map.) (Residue 12: HOH, Nonterminal, was not found in name map.) (Residue 13: HOH, Nonterminal, was not found in name map.) (Residue 14: HOH, Nonterminal, was not found in name map.) (Residue 15: HOH, Nonterminal, was not found in name map.) (Residue 16: HOH, Nonterminal, was not found in name map.) (Residue 17: HOH, Nonterminal, was not found in name map.) (Residue 18: HOH, Nonterminal, was not found in name map.) (Residue 19: HOH, Nonterminal, was not found in name map.) (Residue 20: HOH, Nonterminal, was not found in name map.) (Residue 21: HOH, Nonterminal, was not found in name map.) (Residue 22: HOH, Nonterminal, was not found in name map.) (Residue 23: HOH, Nonterminal, was not found in name map.) (Residue 24: HOH, Nonterminal, was not found in name map.) (Residue 25: HOH, Nonterminal, was not found in name map.) (Residue 26: HOH, Nonterminal, was not found in name map.) (Residue 27: HOH, Nonterminal, was not found in name map.) (Residue 28: HOH, Nonterminal, was not found in name map.) (Residue 29: HOH, Nonterminal, was not found in name map.) (Residue 30: HOH, Nonterminal, was not found in name map.) (Residue 31: HOH, Nonterminal, was not found in name map.) (Residue 32: HOH, Nonterminal, was not found in name map.) (Residue 33: HOH, Nonterminal, was not found in name map.) (Residue 34: HOH, Nonterminal, was not found in name map.) (Residue 35: HOH, Nonterminal, was not found in name map.) (Residue 36: HOH, Nonterminal, was not found in name map.) (Residue 37: HOH, Nonterminal, was not found in name map.) (Residue 38: HOH, Nonterminal, was not found in name map.) (Residue 39: HOH, Nonterminal, was not found in name map.) (Residue 40: HOH, Nonterminal, was not found in name map.) (Residue 41: HOH, Nonterminal, was not found in name map.) (Residue 42: HOH, Nonterminal, was not found in name map.) (Residue 43: HOH, Nonterminal, was not found in name map.) (Residue 44: HOH, Nonterminal, was not found in name map.) (Residue 45: HOH, Nonterminal, was not found in name map.) (Residue 46: HOH, Nonterminal, was not found in name map.) (Residue 47: HOH, Nonterminal, was not found in name map.) (Residue 48: HOH, Nonterminal, was not found in name map.) (Residue 49: HOH, Nonterminal, was not found in name map.) (Residue 50: HOH, Nonterminal, was not found in name map.) (Residue 51: HOH, Nonterminal, was not found in name map.) (Residue 52: HOH, Nonterminal, was not found in name map.) (Residue 53: HOH, Nonterminal, was not found in name map.) (Residue 54: HOH, Nonterminal, was not found in name map.) (Residue 55: HOH, Nonterminal, was not found in name map.) (Residue 56: HOH, Nonterminal, was not found in name map.) (Residue 57: HOH, Nonterminal, was not found in name map.) (Residue 58: HOH, Nonterminal, was not found in name map.) (Residue 59: HOH, Nonterminal, was not found in name map.) (Residue 60: HOH, Nonterminal, was not found in name map.) (Residue 61: HOH, Nonterminal, was not found in name map.) (Residue 62: HOH, Nonterminal, was not found in name map.) (Residue 63: HOH, Nonterminal, was not found in name map.) (Residue 64: HOH, Nonterminal, was not found in name map.) (Residue 65: HOH, Nonterminal, was not found in name map.) (Residue 66: HOH, Nonterminal, was not found in name map.) (Residue 67: HOH, Nonterminal, was not found in name map.) (Residue 68: HOH, Nonterminal, was not found in name map.) (Residue 69: HOH, Nonterminal, was not found in name map.) (Residue 70: HOH, Nonterminal, was not found in name map.) (Residue 71: HOH, Nonterminal, was not found in name map.) (Residue 72: HOH, Nonterminal, was not found in name map.) (Residue 73: HOH, Nonterminal, was not found in name map.) (Residue 74: HOH, Nonterminal, was not found in name map.) (Residue 75: HOH, Nonterminal, was not found in name map.) (Residue 76: HOH, Nonterminal, was not found in name map.) (Residue 77: HOH, Nonterminal, was not found in name map.) (Residue 78: HOH, Nonterminal, was not found in name map.) (Residue 79: HOH, Nonterminal, was not found in name map.) (Residue 80: HOH, Nonterminal, was not found in name map.) (Residue 81: HOH, Nonterminal, was not found in name map.) (Residue 82: HOH, Nonterminal, was not found in name map.) (Residue 83: HOH, Nonterminal, was not found in name map.) (Residue 84: HOH, Nonterminal, was not found in name map.) (Residue 85: HOH, Nonterminal, was not found in name map.) (Residue 86: HOH, Nonterminal, was not found in name map.) (Residue 87: HOH, Nonterminal, was not found in name map.) (Residue 88: HOH, Nonterminal, was not found in name map.) (Residue 89: HOH, Nonterminal, was not found in name map.) (Residue 90: HOH, Nonterminal, was not found in name map.) (Residue 91: HOH, Nonterminal, was not found in name map.) (Residue 92: HOH, Nonterminal, was not found in name map.) (Residue 93: HOH, Nonterminal, was not found in name map.) (Residue 94: HOH, Nonterminal, was not found in name map.) (Residue 95: HOH, Nonterminal, was not found in name map.) (Residue 96: HOH, Nonterminal, was not found in name map.) (Residue 97: HOH, Nonterminal, was not found in name map.) (Residue 98: HOH, Nonterminal, was not found in name map.) (Residue 99: HOH, Nonterminal, was not found in name map.) (Residue 100: HOH, Nonterminal, was not found in name map.) (Residue 101: HOH, Nonterminal, was not found in name map.) (Residue 102: HOH, Nonterminal, was not found in name map.) (Residue 103: HOH, Nonterminal, was not found in name map.) (Residue 104: HOH, Nonterminal, was not found in name map.) (Residue 105: HOH, Nonterminal, was not found in name map.) (Residue 106: HOH, Nonterminal, was not found in name map.) (Residue 107: HOH, Nonterminal, was not found in name map.) (Residue 108: HOH, Nonterminal, was not found in name map.) (Residue 109: HOH, Nonterminal, was not found in name map.) (Residue 110: HOH, Nonterminal, was not found in name map.) (Residue 111: HOH, Nonterminal, was not found in name map.) (Residue 112: HOH, Nonterminal, was not found in name map.) (Residue 113: HOH, Nonterminal, was not found in name map.) (Residue 114: HOH, Nonterminal, was not found in name map.) (Residue 115: HOH, Nonterminal, was not found in name map.) (Residue 116: HOH, Nonterminal, was not found in name map.) (Residue 117: HOH, Nonterminal, was not found in name map.) (Residue 118: HOH, Nonterminal, was not found in name map.) (Residue 119: HOH, Nonterminal, was not found in name map.) (Residue 120: HOH, Nonterminal, was not found in name map.) (Residue 121: HOH, Nonterminal, was not found in name map.) (Residue 122: HOH, Nonterminal, was not found in name map.) (Residue 123: HOH, Nonterminal, was not found in name map.) (Residue 124: HOH, Nonterminal, was not found in name map.) (Residue 125: HOH, Nonterminal, was not found in name map.) (Residue 126: HOH, Nonterminal, was not found in name map.) (Residue 127: HOH, Nonterminal, was not found in name map.) (Residue 128: HOH, Nonterminal, was not found in name map.) (Residue 129: HOH, Nonterminal, was not found in name map.) (Residue 130: HOH, Nonterminal, was not found in name map.) (Residue 131: HOH, Nonterminal, was not found in name map.) (Residue 132: HOH, Nonterminal, was not found in name map.) (Residue 133: HOH, Nonterminal, was not found in name map.) (Residue 134: HOH, Nonterminal, was not found in name map.) (Residue 135: HOH, Nonterminal, was not found in name map.) (Residue 136: HOH, Nonterminal, was not found in name map.) (Residue 137: HOH, Nonterminal, was not found in name map.) (Residue 138: HOH, Nonterminal, was not found in name map.) (Residue 139: HOH, Nonterminal, was not found in name map.) (Residue 140: HOH, Nonterminal, was not found in name map.) (Residue 141: HOH, Nonterminal, was not found in name map.) (Residue 142: HOH, Nonterminal, was not found in name map.) (Residue 143: HOH, Nonterminal, was not found in name map.) (Residue 144: HOH, Nonterminal, was not found in name map.) (Residue 145: HOH, Nonterminal, was not found in name map.) (Residue 146: HOH, Nonterminal, was not found in name map.) (Residue 147: HOH, Nonterminal, was not found in name map.) (Residue 148: HOH, Nonterminal, was not found in name map.) (Residue 149: HOH, Nonterminal, was not found in name map.) (Residue 150: HOH, Nonterminal, was not found in name map.) (Residue 151: HOH, Nonterminal, was not found in name map.) (Residue 152: HOH, Nonterminal, was not found in name map.) (Residue 153: HOH, Nonterminal, was not found in name map.) (Residue 154: HOH, Nonterminal, was not found in name map.) (Residue 155: HOH, Nonterminal, was not found in name map.) (Residue 156: HOH, Nonterminal, was not found in name map.) (Residue 157: HOH, Nonterminal, was not found in name map.) (Residue 158: HOH, Nonterminal, was not found in name map.) (Residue 159: HOH, Nonterminal, was not found in name map.) (Residue 160: HOH, Nonterminal, was not found in name map.) (Residue 161: HOH, Nonterminal, was not found in name map.) (Residue 162: HOH, Nonterminal, was not found in name map.) (Residue 163: HOH, Nonterminal, was not found in name map.) (Residue 164: HOH, Nonterminal, was not found in name map.) (Residue 165: HOH, Terminal/last, was not found in name map.) Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 total atoms in file: 166 Leap added 332 missing atoms according to residue templates: 332 H / lone pairs > > # Add counterions > addions receptor Na+ 5 Adding 5 counter ions to "receptor" using 1A grid Total solute charge: -5.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.87 to 7.87 Box: enclosing: -16.17 -29.62 -12.20 49.94 30.13 69.55 sized: 111.83 98.38 115.80 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 3.13% of box, grid points 65655 (no solvent present) Calculating grid charges charges: 14 sec Placed Na+ in receptor at (5.83, 21.38, 16.80). Placed Na+ in receptor at (14.83, 14.38, -2.20). Placed Na+ in receptor at (33.83, 16.38, 9.80). Placed Na+ in receptor at (29.83, 17.38, 29.80). Placed Na+ in receptor at (2.83, 6.38, -0.20). Done adding ions. > > # Load ligand and parameters. > #loadAmberParams ../../antechamber/PRODRG/DRGFIN.gaff.frcmod > #ligand = loadMol2 ../../antechamber/PRODRG/DRGFIN.gaff.mol2 > > loadAmberParams ../../antechamber/oechem/bosutinib.gaff.frcmod Loading parameters: ../../antechamber/oechem/bosutinib.gaff.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > ligand = loadMol2 ../../antechamber/oechem/bosutinib.gaff.mol2 Loading Mol2 file: ../../antechamber/oechem/bosutinib.gaff.mol2 Reading MOLECULE named 4-(2,4-dichloro-5-methoxy-anilino)-6-methoxy-7-[3-(4-methylpiperazine-1,4-diium-1-yl)propoxy]quinoline-3-carbonitrile > > # Create complex. > complex = combine { receptor closewaters ligand } Sequence: Sequence: Sequence: 4-(2,4-dichloro-5-methoxy-anili > > # Check complex. > check complex Checking 'complex'.... WARNING: The unperturbed charge of the unit: 2.000100 is not zero. Warning: Close contact of 1.147754 angstroms between .R.A and .R.A

Warning: Close contact of 1.108301 angstroms between .R.A and .R.A

Warning: Close contact of 1.478290 angstroms between .R.A and .R.A

Warning: Close contact of 1.308840 angstroms between .R.A and .R.A

Warning: Close contact of 1.040378 angstroms between .R.A and .R.A

Warning: Close contact of 0.827662 angstroms between .R.A and .R.A

Warning: Close contact of 1.284867 angstroms between .R.A and .R.A

Warning: Close contact of 0.954246 angstroms between .R.A and .R.A

Warning: Close contact of 1.068189 angstroms between .R.A and .R.A

Warning: Close contact of 1.166699 angstroms between .R.A and .R.A

Warning: Close contact of 1.394220 angstroms between .R.A and .R.A

Warning: Close contact of 1.479208 angstroms between .R.A and .R.A

Warning: Close contact of 1.139049 angstroms between .R.A and .R.A

Warning: Close contact of 1.156270 angstroms between .R.A and .R.A

Warning: Close contact of 1.142857 angstroms between .R.A and .R.A

Warning: Close contact of 1.423802 angstroms between .R.A and .R.A Warning: Close contact of 0.728908 angstroms between .R.A and .R.A Warning: Close contact of 1.213897 angstroms between .R.A and .R.A

Warning: Close contact of 1.183353 angstroms between .R.A and .R.A Warning: Close contact of 0.979879 angstroms between .R.A and .R.A

Warning: Close contact of 1.365976 angstroms between .R.A

and .R.A

Warning: Close contact of 1.437814 angstroms between .R.A

and .R.A Warning: Close contact of 1.473119 angstroms between .R.A

and .R.A Warning: Close contact of 1.083114 angstroms between .R.A

and .R.A Checking parameters for unit 'complex'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 25 Unit is OK. > > # Report on net charge. > charge ligand Total unperturbed charge: 2.000100 Total perturbed charge: 2.000100 > charge receptor Total unperturbed charge: 0.000000 Total perturbed charge: 0.000000 > charge complex Total unperturbed charge: 2.000100 Total perturbed charge: 2.000100 > > # Solvate ligand, receptor, and complex. > solvatebox ligand TIP3PBOX 12.0 iso Solute vdw bounding box: 24.793 10.238 8.963 Total bounding box for atom centers: 48.793 48.793 48.793 (box expansion for 'iso' is 110.9%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 3 y= 3 z= 3 Adding box at: x=0 y=0 z=0 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=0 y=0 z=1 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=0 y=0 z=2 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=0 y=1 z=0 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=0 y=1 z=1 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=0 y=1 z=2 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=0 y=2 z=0 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=0 y=2 z=1 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=0 y=2 z=2 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=0 z=0 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=1 y=0 z=1 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=1 y=0 z=2 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=1 y=1 z=0 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=1 y=1 z=1 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=1 y=1 z=2 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=1 y=2 z=0 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=1 y=2 z=1 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=1 y=2 z=2 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=0 z=0 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=2 y=0 z=1 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=2 y=0 z=2 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=2 y=1 z=0 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=2 y=1 z=1 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=2 y=1 z=2 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=2 y=2 z=0 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=2 y=2 z=1 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=2 y=2 z=2 Center of solvent box is: -18.774349, -18.774349, -18.774349 Volume: 139742.971 A^3 Total mass 63390.282 amu, Density 0.753 g/cc Added 3489 residues. > solvatebox receptor TIP3PBOX 12.0 iso Solute vdw bounding box: 54.018 43.237 69.159 Total bounding box for atom centers: 93.159 93.159 93.159 (box expansion for 'iso' is 65.4%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 889368.167 A^3 Total mass 461004.090 amu, Density 0.861 g/cc Added 23768 residues. > solvatebox complex TIP3PBOX 12.0 iso Solute vdw bounding box: 53.996 46.998 69.373 Total bounding box for atom centers: 93.373 93.373 93.373 (box expansion for 'iso' is 57.4%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 899785.201 A^3 Total mass 466617.060 amu, Density 0.861 g/cc Added 23884 residues. > > # Write parameters. > saveAmberParm ligand ligand.prmtop ligand.crd Checking Unit. WARNING: The unperturbed charge of the unit: 2.000100 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 16 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 DB8 1 WAT 3489 ) (no restraints) > saveAmberParm receptor receptor.prmtop receptor.crd Checking Unit. 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 ** 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 915 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 CLEU 1 NGLY 1 WAT 23768 ) (no restraints) > saveAmberParm complex complex.prmtop complex.crd Checking Unit. WARNING: The unperturbed charge of the unit: 2.000100 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 ** 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 931 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 CLEU 1 DB8 1 NGLY 1 WAT 24050 ) (no restraints) > > # Exit > quit Quit