log started: Fri Feb 5 15:42:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # 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" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "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" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "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" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/amehta/amber14/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/amehta/amber14/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /home/amehta/amber14/dat/leap/lib/amino12.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: HYP 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 aminoct12.lib Loading library: /home/amehta/amber14/dat/leap/lib/aminoct12.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: CHYP 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 aminont12.lib Loading library: /home/amehta/amber14/dat/leap/lib/aminont12.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 nucleic12.lib Loading library: /home/amehta/amber14/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /home/amehta/amber14/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /home/amehta/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX 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: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 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 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 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" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadamberparams parm10.dat Loading parameters: /home/amehta/amber14/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > loadamberparams frcmod.ff14SB Loading parameters: /home/amehta/amber14/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters > loadamberparams frcmod.ionslm_1264_tip3p Loading parameters: /home/amehta/amber14/dat/leap/parm/frcmod.ionslm_1264_tip3p Reading force field modification type file (frcmod) Reading title: Divalent ion parameters (12_6_4 set) for Particle Mesh Ewald and TIP3P water model from Li and Merz (JCTC 2014, 10, 289-297) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) > loadamberprep GTP_new.prep Loading Prep file: ./GTP_new.prep (UNKNOWN ATOM TYPE: O3) (UNKNOWN ATOM TYPE: O3) (UNKNOWN ATOM TYPE: O3) Loaded UNIT: GTP > loadamberparams frcmod.phos Loading parameters: ./frcmod.phos Reading force field modification type file (frcmod) Reading title: # Modifications to the AMBER94 force field for polyphosphates (UNKNOWN ATOM TYPE: O3) > ml = loadpdb rot.pdb Loading PDB file: ./rot.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: LYS, Nonterminal, was not found in name map.) (Residue 2: ARG, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: VAL, Nonterminal, was not found in name map.) (Residue 6: SER, Nonterminal, was not found in name map.) (Residue 7: ASN, Nonterminal, was not found in name map.) (Residue 8: GLN, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: LYS, Nonterminal, was not found in name map.) (Residue 11: LEU, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: THR, Nonterminal, was not found in name map.) (Residue 14: GLN, Nonterminal, was not found in name map.) (Residue 15: PHE, Nonterminal, was not found in name map.) (Residue 16: GLY, Nonterminal, was not found in name map.) (Residue 17: GLU, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: TYR, Nonterminal, was not found in name map.) (Residue 20: ILE, Nonterminal, was not found in name map.) (Residue 21: GLN, Nonterminal, was not found in name map.) (Residue 22: CYS, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: ARG, Nonterminal, was not found in name map.) (Residue 25: GLU, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: ASN, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: SER, Nonterminal, was not found in name map.) (Residue 32: LYS, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: HIS, Nonterminal, was not found in name map.) (Residue 35: LEU, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: PHE, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: PRO, Nonterminal, was not found in name map.) (Residue 41: ASN, Nonterminal, was not found in name map.) (Residue 42: PHE, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLN, Nonterminal, was not found in name map.) (Residue 45: ASN, Nonterminal, was not found in name map.) (Residue 46: PRO, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: HIS, Nonterminal, was not found in name map.) (Residue 52: SER, Nonterminal, was not found in name map.) (Residue 53: GLU, Nonterminal, was not found in name map.) (Residue 54: CYS, Nonterminal, was not found in name map.) (Residue 55: LEU, Nonterminal, was not found in name map.) (Residue 56: THR, Nonterminal, was not found in name map.) (Residue 57: GLY, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: ALA, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: SER, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: LYS, Nonterminal, was not found in name map.) (Residue 65: CYS, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: CYS, Nonterminal, was not found in name map.) (Residue 68: GLY, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: ALA, Nonterminal, was not found in name map.) (Residue 71: LEU, Nonterminal, was not found in name map.) (Residue 72: GLN, Nonterminal, was not found in name map.) (Residue 73: MET, Nonterminal, was not found in name map.) (Residue 74: ALA, Nonterminal, was not found in name map.) (Residue 75: LEU, Nonterminal, was not found in name map.) (Residue 76: GLU, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ILE, Nonterminal, was not found in name map.) (Residue 79: SER, Nonterminal, was not found in name map.) (Residue 80: LYS, Nonterminal, was not found in name map.) (Residue 81: GLU, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: GLY, Nonterminal, was not found in name map.) (Residue 84: LEU, Nonterminal, was not found in name map.) (Residue 85: VAL, 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: LEU, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: GLN, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: GLY, Nonterminal, was not found in name map.) (Residue 93: ARG, Nonterminal, was not found in name map.) (Residue 94: GLY, Nonterminal, was not found in name map.) (Residue 95: ILE, Nonterminal, was not found in name map.) (Residue 96: GLY, Nonterminal, was not found in name map.) (Residue 97: LEU, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: ASN, Nonterminal, was not found in name map.) (Residue 100: LYS, Nonterminal, was not found in name map.) (Residue 101: VAL, Nonterminal, was not found in name map.) (Residue 102: ASN, Nonterminal, was not found in name map.) (Residue 103: ALA, Nonterminal, was not found in name map.) (Residue 104: TYR, Nonterminal, was not found in name map.) (Residue 105: ALA, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: GLN, Nonterminal, was not found in name map.) (Residue 108: ASP, Nonterminal, was not found in name map.) (Residue 109: LYS, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: TYR, Nonterminal, was not found in name map.) (Residue 112: ASP, Nonterminal, was not found in name map.) (Residue 113: THR, Nonterminal, was not found in name map.) (Residue 114: ILE, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: ALA, Nonterminal, was not found in name map.) (Residue 117: ASN, Nonterminal, was not found in name map.) (Residue 118: GLU, Nonterminal, was not found in name map.) (Residue 119: MET, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: GLY, Nonterminal, was not found in name map.) (Residue 122: PHE, Nonterminal, was not found in name map.) (Residue 123: LYS, Nonterminal, was not found in name map.) (Residue 124: ASP, Nonterminal, was not found in name map.) (Residue 125: ASP, Nonterminal, was not found in name map.) (Residue 126: GLU, Nonterminal, was not found in name map.) (Residue 127: ARG, Nonterminal, was not found in name map.) (Residue 128: ASP, Nonterminal, was not found in name map.) (Residue 129: TYR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: ALA, Nonterminal, was not found in name map.) (Residue 133: GLY, Nonterminal, was not found in name map.) (Residue 134: GLU, Nonterminal, was not found in name map.) (Residue 135: ILE, Nonterminal, was not found in name map.) (Residue 136: LEU, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: TYR, Nonterminal, was not found in name map.) (Residue 139: TYR, Nonterminal, was not found in name map.) (Residue 140: ARG, Nonterminal, was not found in name map.) (Residue 141: ILE, Nonterminal, was not found in name map.) (Residue 142: LYS, Nonterminal, was not found in name map.) (Residue 143: LYS, Nonterminal, was not found in name map.) (Residue 144: MET, Nonterminal, was not found in name map.) (Residue 145: ARG, Nonterminal, was not found in name map.) (Residue 146: LEU, Nonterminal, was not found in name map.) (Residue 147: LEU, Nonterminal, was not found in name map.) (Residue 148: THR, Nonterminal, was not found in name map.) (Residue 149: ASN, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: PRO, Nonterminal, was not found in name map.) (Residue 152: LYS, Nonterminal, was not found in name map.) (Residue 153: LYS, Nonterminal, was not found in name map.) (Residue 154: ILE, Nonterminal, was not found in name map.) (Residue 155: ALA, Nonterminal, was not found in name map.) (Residue 156: ALA, Nonterminal, was not found in name map.) (Residue 157: LEU, Nonterminal, was not found in name map.) (Residue 158: GLU, Nonterminal, was not found in name map.) (Residue 159: LYS, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: THR, Nonterminal, was not found in name map.) (Residue 165: ARG, Nonterminal, was not found in name map.) (Residue 166: GLU, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: CYS, Nonterminal, was not found in name map.) (Residue 172: ALA, Nonterminal, was not found in name map.) (Residue 173: ASN, Nonterminal, was not found in name map.) (Residue 174: GLU, Nonterminal, was not found in name map.) (Residue 175: HIS, Nonterminal, was not found in name map.) (Residue 176: ASN, Nonterminal, was not found in name map.) (Residue 177: GLN, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: TYR, Nonterminal, was not found in name map.) (Residue 180: LEU, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: LYS, Nonterminal, was not found in name map.) (Residue 184: LYS, Nonterminal, was not found in name map.) (Residue 185: LEU, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: MET, Nonterminal, was not found in name map.) (Residue 188: GLY, Nonterminal, was not found in name map.) (Residue 189: HIS, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 191 to: CLEU. Mapped residue MET, term: Terminal/beginning, seq. number: 192 to: NMET. (Residue 193: LYS, Nonterminal, was not found in name map.) (Residue 194: ARG, Nonterminal, was not found in name map.) (Residue 195: LEU, Nonterminal, was not found in name map.) (Residue 196: GLU, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: SER, Nonterminal, was not found in name map.) (Residue 199: ASN, Nonterminal, was not found in name map.) (Residue 200: GLN, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LYS, Nonterminal, was not found in name map.) (Residue 203: LEU, Nonterminal, was not found in name map.) (Residue 204: PRO, Nonterminal, was not found in name map.) (Residue 205: THR, Nonterminal, was not found in name map.) (Residue 206: GLN, Nonterminal, was not found in name map.) (Residue 207: PHE, Nonterminal, was not found in name map.) (Residue 208: GLY, Nonterminal, was not found in name map.) (Residue 209: GLU, Nonterminal, was not found in name map.) (Residue 210: PHE, Nonterminal, was not found in name map.) (Residue 211: TYR, Nonterminal, was not found in name map.) (Residue 212: ILE, Nonterminal, was not found in name map.) (Residue 213: GLN, Nonterminal, was not found in name map.) (Residue 214: CYS, Nonterminal, was not found in name map.) (Residue 215: PHE, Nonterminal, was not found in name map.) (Residue 216: ARG, Nonterminal, was not found in name map.) (Residue 217: GLU, Nonterminal, was not found in name map.) (Residue 218: LYS, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: ASN, Nonterminal, was not found in name map.) (Residue 222: GLY, Nonterminal, was not found in name map.) (Residue 223: SER, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ASP, Nonterminal, was not found in name map.) (Residue 226: HIS, Nonterminal, was not found in name map.) (Residue 227: LEU, Nonterminal, was not found in name map.) (Residue 228: VAL, Nonterminal, was not found in name map.) (Residue 229: VAL, Nonterminal, was not found in name map.) (Residue 230: PHE, Nonterminal, was not found in name map.) (Residue 231: THR, Nonterminal, was not found in name map.) (Residue 232: PRO, Nonterminal, was not found in name map.) (Residue 233: ASN, Nonterminal, was not found in name map.) (Residue 234: PHE, Nonterminal, was not found in name map.) (Residue 235: SER, Nonterminal, was not found in name map.) (Residue 236: GLN, Nonterminal, was not found in name map.) (Residue 237: ASN, Nonterminal, was not found in name map.) (Residue 238: PRO, Nonterminal, was not found in name map.) (Residue 239: LEU, Nonterminal, was not found in name map.) (Residue 240: VAL, Nonterminal, was not found in name map.) (Residue 241: ARG, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: HIS, Nonterminal, was not found in name map.) (Residue 244: SER, Nonterminal, was not found in name map.) (Residue 245: GLU, Nonterminal, was not found in name map.) (Residue 246: CYS, Nonterminal, was not found in name map.) (Residue 247: LEU, Nonterminal, was not found in name map.) (Residue 248: THR, Nonterminal, was not found in name map.) (Residue 249: GLY, Nonterminal, was not found in name map.) (Residue 250: ASP, Nonterminal, was not found in name map.) (Residue 251: ALA, Nonterminal, was not found in name map.) (Residue 252: LEU, Nonterminal, was not found in name map.) (Residue 253: GLY, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: GLN, Nonterminal, was not found in name map.) (Residue 256: LYS, Nonterminal, was not found in name map.) (Residue 257: CYS, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: CYS, Nonterminal, was not found in name map.) (Residue 260: GLY, Nonterminal, was not found in name map.) (Residue 261: GLY, Nonterminal, was not found in name map.) (Residue 262: ALA, Nonterminal, was not found in name map.) (Residue 263: LEU, Nonterminal, was not found in name map.) (Residue 264: GLN, Nonterminal, was not found in name map.) (Residue 265: MET, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: GLU, Nonterminal, was not found in name map.) (Residue 269: ARG, Nonterminal, was not found in name map.) (Residue 270: ILE, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: LYS, Nonterminal, was not found in name map.) (Residue 273: GLU, Nonterminal, was not found in name map.) (Residue 274: GLY, Nonterminal, was not found in name map.) (Residue 275: GLY, Nonterminal, was not found in name map.) (Residue 276: LEU, Nonterminal, was not found in name map.) (Residue 277: VAL, Nonterminal, was not found in name map.) (Residue 278: ILE, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ARG, Nonterminal, was not found in name map.) (Residue 282: GLN, Nonterminal, was not found in name map.) (Residue 283: GLU, Nonterminal, was not found in name map.) (Residue 284: GLY, Nonterminal, was not found in name map.) (Residue 285: ARG, Nonterminal, was not found in name map.) (Residue 286: GLY, Nonterminal, was not found in name map.) (Residue 287: ILE, Nonterminal, was not found in name map.) (Residue 288: GLY, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: PHE, Nonterminal, was not found in name map.) (Residue 291: ASN, Nonterminal, was not found in name map.) (Residue 292: LYS, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: ASN, Nonterminal, was not found in name map.) (Residue 295: ALA, Nonterminal, was not found in name map.) (Residue 296: TYR, Nonterminal, was not found in name map.) (Residue 297: ALA, Nonterminal, was not found in name map.) (Residue 298: LEU, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: ASP, Nonterminal, was not found in name map.) (Residue 301: LYS, Nonterminal, was not found in name map.) (Residue 302: GLY, Nonterminal, was not found in name map.) (Residue 303: TYR, Nonterminal, was not found in name map.) (Residue 304: ASP, Nonterminal, was not found in name map.) (Residue 305: THR, Nonterminal, was not found in name map.) (Residue 306: ILE, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: ALA, Nonterminal, was not found in name map.) (Residue 309: ASN, Nonterminal, was not found in name map.) (Residue 310: GLU, Nonterminal, was not found in name map.) (Residue 311: MET, Nonterminal, was not found in name map.) (Residue 312: ILE, Nonterminal, was not found in name map.) (Residue 313: GLY, Nonterminal, was not found in name map.) (Residue 314: PHE, Nonterminal, was not found in name map.) (Residue 315: LYS, Nonterminal, was not found in name map.) (Residue 316: ASP, Nonterminal, was not found in name map.) (Residue 317: ASP, Nonterminal, was not found in name map.) (Residue 318: GLU, Nonterminal, was not found in name map.) (Residue 319: ARG, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: SER, Nonterminal, was not found in name map.) (Residue 323: VAL, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: GLY, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: ILE, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: GLU, Nonterminal, was not found in name map.) (Residue 330: TYR, Nonterminal, was not found in name map.) (Residue 331: TYR, Nonterminal, was not found in name map.) (Residue 332: ARG, Nonterminal, was not found in name map.) (Residue 333: ILE, Nonterminal, was not found in name map.) (Residue 334: LYS, Nonterminal, was not found in name map.) (Residue 335: LYS, Nonterminal, was not found in name map.) (Residue 336: MET, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: LEU, Nonterminal, was not found in name map.) (Residue 340: THR, Nonterminal, was not found in name map.) (Residue 341: ASN, Nonterminal, was not found in name map.) (Residue 342: ASN, Nonterminal, was not found in name map.) (Residue 343: PRO, Nonterminal, was not found in name map.) (Residue 344: LYS, Nonterminal, was not found in name map.) (Residue 345: LYS, Nonterminal, was not found in name map.) (Residue 346: ILE, Nonterminal, was not found in name map.) (Residue 347: ALA, Nonterminal, was not found in name map.) (Residue 348: ALA, Nonterminal, was not found in name map.) (Residue 349: LEU, Nonterminal, was not found in name map.) (Residue 350: GLU, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: TYR, Nonterminal, was not found in name map.) (Residue 353: ALA, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: VAL, Nonterminal, was not found in name map.) (Residue 356: THR, Nonterminal, was not found in name map.) (Residue 357: ARG, Nonterminal, was not found in name map.) (Residue 358: GLU, Nonterminal, was not found in name map.) (Residue 359: SER, Nonterminal, was not found in name map.) (Residue 360: LEU, Nonterminal, was not found in name map.) (Residue 361: ILE, Nonterminal, was not found in name map.) (Residue 362: VAL, Nonterminal, was not found in name map.) (Residue 363: CYS, Nonterminal, was not found in name map.) (Residue 364: ALA, Nonterminal, was not found in name map.) (Residue 365: ASN, Nonterminal, was not found in name map.) (Residue 366: GLU, Nonterminal, was not found in name map.) (Residue 367: HIS, Nonterminal, was not found in name map.) (Residue 368: ASN, Nonterminal, was not found in name map.) (Residue 369: GLN, Nonterminal, was not found in name map.) (Residue 370: GLY, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: LEU, Nonterminal, was not found in name map.) (Residue 373: GLU, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: LYS, Nonterminal, was not found in name map.) (Residue 376: LYS, Nonterminal, was not found in name map.) (Residue 377: LEU, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: MET, Nonterminal, was not found in name map.) (Residue 380: GLY, Nonterminal, was not found in name map.) (Residue 381: HIS, Nonterminal, was not found in name map.) (Residue 382: LEU, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 383 to: CLEU. (Residue 384: ZN, Terminal/last, was not found in name map.) (Residue 385: MG, Terminal/last, was not found in name map.) (Residue 386: GTP, Terminal/last, was not found in name map.) (Residue 387: ZN, Terminal/last, was not found in name map.) (Residue 388: MG, Terminal/last, was not found in name map.) (Residue 389: GTP, Terminal/last, was not found in name map.) Joining NMET - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - SER Joining SER - ASN Joining ASN - GLN Joining GLN - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - PRO Joining PRO - THR Joining THR - GLN Joining GLN - PHE Joining PHE - GLY Joining GLY - GLU Joining GLU - PHE Joining PHE - TYR Joining TYR - ILE Joining ILE - GLN Joining GLN - CYS Joining CYS - PHE Joining PHE - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - GLY Joining GLY - SER Joining SER - ASN Joining ASN - GLY Joining GLY - SER Joining SER - LYS Joining LYS - ASP Joining ASP - HIE Joining HIE - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - PHE Joining PHE - THR Joining THR - PRO Joining PRO - ASN Joining ASN - PHE Joining PHE - SER Joining SER - GLN Joining GLN - ASN Joining ASN - PRO Joining PRO - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - HIE Joining HIE - SER Joining SER - GLU Joining GLU - CYS Joining CYS - LEU Joining LEU - THR Joining THR - GLY Joining GLY - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - GLY Joining GLY - SER Joining SER - GLN Joining GLN - LYS Joining LYS - CYS Joining CYS - ASP Joining ASP - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - MET Joining MET - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - SER Joining SER - LYS Joining LYS - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - VAL Joining VAL - ILE Joining ILE - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - ASN Joining ASN - LYS Joining LYS - VAL Joining VAL - ASN Joining ASN - ALA Joining ALA - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - LYS Joining LYS - GLY Joining GLY - TYR Joining TYR - ASP Joining ASP - THR Joining THR - ILE Joining ILE - GLN Joining GLN - ALA Joining ALA - ASN Joining ASN - GLU Joining GLU - MET Joining MET - ILE Joining ILE - GLY Joining GLY - PHE Joining PHE - LYS Joining LYS - ASP Joining ASP - ASP Joining ASP - GLU Joining GLU - ARG Joining ARG - ASP Joining ASP - TYR Joining TYR - SER Joining SER - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - TYR Joining TYR - TYR Joining TYR - ARG Joining ARG - ILE Joining ILE - LYS Joining LYS - LYS Joining LYS - MET Joining MET - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - THR Joining THR - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - LYS Joining LYS - LYS Joining LYS - ILE Joining ILE - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - LYS Joining LYS - TYR Joining TYR - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ARG Joining ARG - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - CYS Joining CYS - ALA Joining ALA - ASN Joining ASN - GLU Joining GLU - HIE Joining HIE - ASN Joining ASN - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - MET Joining MET - GLY Joining GLY - HIE Joining HIE - LEU Joining LEU - CLEU Added missing heavy atom: .R.A Joining NMET - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - SER Joining SER - ASN Joining ASN - GLN Joining GLN - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - PRO Joining PRO - THR Joining THR - GLN Joining GLN - PHE Joining PHE - GLY Joining GLY - GLU Joining GLU - PHE Joining PHE - TYR Joining TYR - ILE Joining ILE - GLN Joining GLN - CYS Joining CYS - PHE Joining PHE - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - GLY Joining GLY - SER Joining SER - ASN Joining ASN - GLY Joining GLY - SER Joining SER - LYS Joining LYS - ASP Joining ASP - HIE Joining HIE - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - PHE Joining PHE - THR Joining THR - PRO Joining PRO - ASN Joining ASN - PHE Joining PHE - SER Joining SER - GLN Joining GLN - ASN Joining ASN - PRO Joining PRO - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - LEU Joining LEU - HIE Joining HIE - SER Joining SER - GLU Joining GLU - CYS Joining CYS - LEU Joining LEU - THR Joining THR - GLY Joining GLY - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - GLY Joining GLY - SER Joining SER - GLN Joining GLN - LYS Joining LYS - CYS Joining CYS - ASP Joining ASP - CYS Joining CYS - GLY Joining GLY - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - MET Joining MET - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - SER Joining SER - LYS Joining LYS - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - VAL Joining VAL - ILE Joining ILE - TYR Joining TYR - LEU Joining LEU - ARG Joining ARG - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - ASN Joining ASN - LYS Joining LYS - VAL Joining VAL - ASN Joining ASN - ALA Joining ALA - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - LYS Joining LYS - GLY Joining GLY - TYR Joining TYR - ASP Joining ASP - THR Joining THR - ILE Joining ILE - GLN Joining GLN - ALA Joining ALA - ASN Joining ASN - GLU Joining GLU - MET Joining MET - ILE Joining ILE - GLY Joining GLY - PHE Joining PHE - LYS Joining LYS - ASP Joining ASP - ASP Joining ASP - GLU Joining GLU - ARG Joining ARG - ASP Joining ASP - TYR Joining TYR - SER Joining SER - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - TYR Joining TYR - TYR Joining TYR - ARG Joining ARG - ILE Joining ILE - LYS Joining LYS - LYS Joining LYS - MET Joining MET - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - THR Joining THR - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - LYS Joining LYS - LYS Joining LYS - ILE Joining ILE - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - LYS Joining LYS - TYR Joining TYR - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ARG Joining ARG - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ILE Joining ILE - VAL Joining VAL - CYS Joining CYS - ALA Joining ALA - ASN Joining ASN - GLU Joining GLU - HIE Joining HIE - ASN Joining ASN - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - MET Joining MET - GLY Joining GLY - HIE Joining HIE - LEU Joining LEU - CLEU Added missing heavy atom: .R.A total atoms in file: 3112 Leap added 3100 missing atoms according to residue templates: 2 Heavy 3098 H / lone pairs > check ml Checking 'ml'.... WARNING: The unperturbed charge of the unit: 6.000000 is not zero. Warning: Close contact of 1.424929 angstroms between .R.A and .R.A Warning: Close contact of 1.317013 angstroms between .R.A and .R.A Warning: Close contact of 1.351078 angstroms between .R.A and .R.A Warning: Close contact of 0.748084 angstroms between .R.A and .R.A Warning: Close contact of 1.055035 angstroms between .R.A and .R.A Warning: Close contact of 1.353753 angstroms between .R.A and .R.A Warning: Close contact of 0.666796 angstroms between .R.A and .R.A Warning: Close contact of 0.615042 angstroms between .R.A and .R.A Warning: Close contact of 0.839070 angstroms between .R.A and .R.A Warning: Close contact of 1.247478 angstroms between .R.A and .R.A Warning: Close contact of 1.178365 angstroms between .R.A and .R.A Warning: Close contact of 1.126640 angstroms between .R.A and .R.A Warning: Close contact of 1.099003 angstroms between .R.A and .R.A Warning: Close contact of 0.408410 angstroms between .R.A and .R.A Warning: Close contact of 1.322069 angstroms between .R.A and .R.A Warning: Close contact of 1.438242 angstroms between .R.A and .R.A Warning: Close contact of 1.398232 angstroms between .R.A and .R.A Warning: Close contact of 0.704955 angstroms between .R.A and .R.A Warning: Close contact of 1.309206 angstroms between .R.A and .R.A Warning: Close contact of 1.183549 angstroms between .R.A and .R.A Warning: Close contact of 0.967225 angstroms between .R.A and .R.A Warning: Close contact of 1.260916 angstroms between .R.A and .R.A Warning: Close contact of 1.351874 angstroms between .R.A and .R.A Warning: Close contact of 1.314517 angstroms between .R.A and .R.A Warning: Close contact of 1.197172 angstroms between .R.A and .R.A Warning: Close contact of 0.787851 angstroms between .R.A and .R.A Warning: Close contact of 1.129677 angstroms between .R.A and .R.A Warning: Close contact of 1.495954 angstroms between .R.A and .R.A Warning: Close contact of 0.986542 angstroms between .R.A and .R.A Warning: Close contact of 0.677499 angstroms between .R.A and .R.A Warning: Close contact of 1.234807 angstroms between .R.A and .R.A Warning: Close contact of 0.997159 angstroms between .R.A and .R.A Warning: Close contact of 1.291884 angstroms between .R.A and .R.A Warning: Close contact of 1.183637 angstroms between .R.A and .R.A Warning: Close contact of 1.289546 angstroms between .R.A and .R.A Warning: Close contact of 1.477642 angstroms between .R.A and .R.A Warning: Close contact of 0.428716 angstroms between .R.A and .R.A Warning: Close contact of 1.376152 angstroms between .R.A and .R.A Warning: Close contact of 1.296863 angstroms between .R.A and .R.A Warning: Close contact of 1.186694 angstroms between .R.A and .R.A Warning: Close contact of 0.775658 angstroms between .R.A and .R.A Warning: Close contact of 1.173541 angstroms between .R.A and .R.A Warning: Close contact of 1.383837 angstroms between .R.A and .R.A Warning: Close contact of 1.380438 angstroms between .R.A and .R.A Warning: Close contact of 1.218242 angstroms between .R.A and .R.A Warning: Close contact of 1.229396 angstroms between .R.A and .R.A Warning: Close contact of 1.324303 angstroms between .R.A and .R.A Warning: Close contact of 1.231158 angstroms between .R.A and .R.A Warning: Close contact of 1.001274 angstroms between .R.A and .R.A Warning: Close contact of 0.732988 angstroms between .R.A and .R.A Warning: Close contact of 0.588817 angstroms between .R.A and .R.A Warning: Close contact of 1.399511 angstroms between .R.A and .R.A Warning: Close contact of 0.779332 angstroms between .R.A and .R.A Warning: Close contact of 1.225725 angstroms between .R.A and .R.A Warning: Close contact of 1.175649 angstroms between .R.A and .R.A Warning: Close contact of 1.140299 angstroms between .R.A and .R.A Warning: Close contact of 0.594731 angstroms between .R.A and .R.A Warning: Close contact of 1.273396 angstroms between .R.A and .R.A Warning: Close contact of 0.302028 angstroms between .R.A and .R.A Warning: Close contact of 1.121561 angstroms between .R.A and .R.A Warning: Close contact of 1.341017 angstroms between .R.A and .R.A Warning: Close contact of 1.445922 angstroms between .R.A and .R.A Warning: Close contact of 1.169434 angstroms between .R.A and .R.A Warning: Close contact of 1.448618 angstroms between .R.A and .R.A Warning: Close contact of 1.424768 angstroms between .R.A and .R.A Warning: Close contact of 1.260430 angstroms between .R.A and .R.A Warning: Close contact of 1.352269 angstroms between .R.A and .R.A Warning: Close contact of 1.287555 angstroms between .R.A and .R.A Warning: Close contact of 1.345107 angstroms between .R.A and .R.A Warning: Close contact of 1.306224 angstroms between .R.A and .R.A Warning: Close contact of 1.412798 angstroms between .R.A and .R.A Warning: Close contact of 1.419683 angstroms between .R.A and .R.A Warning: Close contact of 1.290029 angstroms between .R.A and .R.A Warning: Close contact of 1.322789 angstroms between .R.A and .R.A Warning: Close contact of 0.401917 angstroms between .R.A and .R.A Warning: Close contact of 1.029352 angstroms between .R.A and .R.A Warning: Close contact of 1.340502 angstroms between .R.A and .R.A Warning: Close contact of 1.445557 angstroms between .R.A and .R.A Warning: Close contact of 1.169118 angstroms between .R.A and .R.A Warning: Close contact of 1.447952 angstroms between .R.A and .R.A Checking parameters for unit 'ml'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 81 Unit is OK. > solvateoct ml TIP3PBOX 12 Scaling up box by a factor of 1.257992 to meet diagonal cut criterion Solute vdw bounding box: 62.155 45.706 70.291 Total bounding box for atom centers: 100.483 100.483 100.483 (box expansion for 'iso' is 44.1%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 522575.707 A^3 (oct) Total mass 283293.990 amu, Density 0.900 g/cc Added 13246 residues. > addions ml Cl- 0 6 Cl- ions required to neutralize. Using default radius 1.50 for ion Cl- Adding 6 counter ions to "ml" using 1A grid Total solute charge: 6.00 Max atom radius: 2.10 Grid extends from solute vdw + 2.87 to 8.97 Box: enclosing: -37.89 -40.90 -37.30 39.34 40.19 35.19 sized: 90.11 87.10 90.70 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 3.74% of box, grid points 78440 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 23 sec (Replacing solvent molecule) Placed Cl- in ml at (-29.78, 1.32, 6.35). (Replacing solvent molecule) Placed Cl- in ml at (6.88, 13.80, 25.18). (Replacing solvent molecule) Placed Cl- in ml at (-3.99, 1.29, 10.85). (Replacing solvent molecule) Placed Cl- in ml at (20.58, 18.51, -15.39). (Replacing solvent molecule) Placed Cl- in ml at (-5.27, -29.68, -7.12). (Replacing solvent molecule) Placed Cl- in ml at (-8.60, 7.93, 6.64). Done adding ions. > saveamberparm ml rot-12-6-4.prmtop rot-12-6-4.inpcrd Checking Unit. Building topology. Building atom parameters. For atom: .R.A Could not find vdW (or other) parameters for type: Cl- For atom: .R.A Could not find vdW (or other) parameters for type: Cl- For atom: .R.A Could not find vdW (or other) parameters for type: Cl- For atom: .R.A Could not find vdW (or other) parameters for type: Cl- For atom: .R.A Could not find vdW (or other) parameters for type: Cl- For atom: .R.A Could not find vdW (or other) parameters for type: Cl- Parameter file was not saved. > loadamberparams frcmod.ionsff99_tip3p Loading parameters: /home/amehta/amber14/dat/leap/parm/frcmod.ionsff99_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for TIP3P water from Aqvist (adapeted) in parm99.dat > saveamberparm ml rot-12-6-4.prmtop rot-12-6-4.inpcrd 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 NC-CB-CB-N* atoms are: N3 C5 C4 N9 ** Warning: No sp2 improper torsion term for NB-C-CB-CB atoms are: N7 C6 C5 C4 ** Warning: No sp2 improper torsion term for NC-CB-CB-N* atoms are: N3 C5 C4 N9 ** Warning: No sp2 improper torsion term for NB-C-CB-CB atoms are: N7 C6 C5 C4 old PREP-specified impropers: : C8 C4 N9 C1' : C5 N1 C6 O6 : C6 C2 N1 H1 : C2 H21 N2 H22 : N7 N9 C8 H8 : N1 N3 C2 N2 : C8 C4 N9 C1' : C5 N1 C6 O6 : C6 C2 N1 H1 : C2 H21 N2 H22 : N7 N9 C8 H8 : N1 N3 C2 N2 total 1214 improper torsions applied 12 improper torsions in old prep form Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 2 NMET 2 WAT 13240 ) (no restraints) > quit Quit