log started: Fri Jul 8 22:50:47 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/lea/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/lea/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/lea/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/lea/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/lea/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/lea/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/lea/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/lea/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 > > source leaprc.gaff ----- Source: /home/lea/amber14//dat/leap/cmd/leaprc.gaff ----- Source of /home/lea/amber14//dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Jul 8 22:50:48 2016 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" } >> { "cz" "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" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "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: /home/lea/amber14//dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.7, Nov 2013) > > loadoff Cup.lib Loading library: ./Cup.lib Loading: MOL > loadoff o2.lib Loading library: ./o2.lib Loading: O2 > loadoff cid.lib Loading library: ./cid.lib Loading: CID > loadoff hit.lib Loading library: ./hit.lib Loading: HIT > addAtomTypes{ > { "CU" "Cu" "sp3"} > { "Omu2" "O" "sp2" } > } > loadamberparams mix.frcmod Loading parameters: ./mix.frcmod Reading force field modification type file (frcmod) Reading title: Adapted form Kollman and amino10.in for PPO > x = loadpdb PPO_24jun.pdb Loading PDB file: ./PPO_24jun.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: ACE, Terminal/beginning, was not found in name map.) (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: ILE, Nonterminal, was not found in name map.) (Residue 3: GLN, Nonterminal, was not found in name map.) (Residue 4: ALA, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: ILE, Nonterminal, was not found in name map.) (Residue 8: SER, Nonterminal, was not found in name map.) (Residue 9: LYS, Nonterminal, was not found in name map.) (Residue 10: CYX, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: PRO, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: PRO, Nonterminal, was not found in name map.) (Residue 19: PRO, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ALA, Nonterminal, was not found in name map.) (Residue 22: VAL, Nonterminal, was not found in name map.) (Residue 23: VAL, Nonterminal, was not found in name map.) (Residue 24: ASP, Nonterminal, was not found in name map.) (Residue 25: ASN, Nonterminal, was not found in name map.) (Residue 26: CYX, Nonterminal, was not found in name map.) (Residue 27: CYX, Nonterminal, was not found in name map.) (Residue 28: PRO, Nonterminal, was not found in name map.) (Residue 29: PRO, Nonterminal, was not found in name map.) (Residue 30: VAL, Nonterminal, was not found in name map.) (Residue 31: ALA, Nonterminal, was not found in name map.) (Residue 32: SER, Nonterminal, was not found in name map.) (Residue 33: ASN, Nonterminal, was not found in name map.) (Residue 34: ILE, Nonterminal, was not found in name map.) (Residue 35: VAL, Nonterminal, was not found in name map.) (Residue 36: ASP, Nonterminal, was not found in name map.) (Residue 37: TYR, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: PRO, Nonterminal, was not found in name map.) (Residue 41: ALA, Nonterminal, was not found in name map.) (Residue 42: VAL, Nonterminal, was not found in name map.) (Residue 43: THR, Nonterminal, was not found in name map.) (Residue 44: THR, Nonterminal, was not found in name map.) (Residue 45: MET, Nonterminal, was not found in name map.) (Residue 46: LYS, Nonterminal, was not found in name map.) (Residue 47: VAL, Nonterminal, was not found in name map.) (Residue 48: ARG, Nonterminal, was not found in name map.) (Residue 49: PRO, Nonterminal, was not found in name map.) (Residue 50: ALA, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: HIE, 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: ASP, Nonterminal, was not found in name map.) (Residue 56: LYS, Nonterminal, was not found in name map.) (Residue 57: ASP, Nonterminal, was not found in name map.) (Residue 58: ALA, Nonterminal, was not found in name map.) (Residue 59: ILE, Nonterminal, was not found in name map.) (Residue 60: ALA, Nonterminal, was not found in name map.) (Residue 61: LYS, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: ALA, Nonterminal, was not found in name map.) (Residue 64: LYS, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: VAL, Nonterminal, was not found in name map.) (Residue 67: GLU, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: MET, Nonterminal, was not found in name map.) (Residue 70: LYS, Nonterminal, was not found in name map.) (Residue 71: ALA, Nonterminal, was not found in name map.) (Residue 72: LEU, Nonterminal, was not found in name map.) (Residue 73: PRO, Nonterminal, was not found in name map.) (Residue 74: ALA, Nonterminal, was not found in name map.) (Residue 75: ASP, Nonterminal, was not found in name map.) (Residue 76: ASP, Nonterminal, was not found in name map.) (Residue 77: PRO, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: ASN, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: TYR, Nonterminal, was not found in name map.) (Residue 82: GLN, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: ALA, Nonterminal, was not found in name map.) (Residue 85: LEU, Nonterminal, was not found in name map.) (Residue 86: VAL, Nonterminal, was not found in name map.) (Residue 87: HID, Nonterminal, was not found in name map.) (Residue 88: CYX, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: CID, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: GLY, Nonterminal, was not found in name map.) (Residue 94: GLY, Nonterminal, was not found in name map.) (Residue 95: TYR, Nonterminal, was not found in name map.) (Residue 96: ASP, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: VAL, Nonterminal, was not found in name map.) (Residue 99: ASN, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: PRO, Nonterminal, was not found in name map.) (Residue 102: ASP, Nonterminal, was not found in name map.) (Residue 103: GLN, Nonterminal, was not found in name map.) (Residue 104: GLU, Nonterminal, was not found in name map.) (Residue 105: ILE, Nonterminal, was not found in name map.) (Residue 106: GLN, Nonterminal, was not found in name map.) (Residue 107: VAL, Nonterminal, was not found in name map.) (Residue 108: HIT, Nonterminal, was not found in name map.) (Residue 109: ASN, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: TRP, Nonterminal, was not found in name map.) (Residue 112: LEU, Nonterminal, was not found in name map.) (Residue 113: PHE, Nonterminal, was not found in name map.) (Residue 114: PHE, Nonterminal, was not found in name map.) (Residue 115: PRO, Nonterminal, was not found in name map.) (Residue 116: PHE, Nonterminal, was not found in name map.) (Residue 117: HID, Nonterminal, was not found in name map.) (Residue 118: ARG, Nonterminal, was not found in name map.) (Residue 119: TRP, Nonterminal, was not found in name map.) (Residue 120: TYR, Nonterminal, was not found in name map.) (Residue 121: LEU, Nonterminal, was not found in name map.) (Residue 122: TYR, Nonterminal, was not found in name map.) (Residue 123: PHE, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLU, Nonterminal, was not found in name map.) (Residue 126: ARG, Nonterminal, was not found in name map.) (Residue 127: ILE, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: GLY, Nonterminal, was not found in name map.) (Residue 130: LYS, Nonterminal, was not found in name map.) (Residue 131: LEU, Nonterminal, was not found in name map.) (Residue 132: ILE, Nonterminal, was not found in name map.) (Residue 133: GLY, Nonterminal, was not found in name map.) (Residue 134: ASP, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: SER, Nonterminal, was not found in name map.) (Residue 137: PHE, Nonterminal, was not found in name map.) (Residue 138: GLY, Nonterminal, was not found in name map.) (Residue 139: LEU, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: PHE, Nonterminal, was not found in name map.) (Residue 142: TRP, Nonterminal, was not found in name map.) (Residue 143: ASN, Nonterminal, was not found in name map.) (Residue 144: TRP, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: ASN, Nonterminal, was not found in name map.) (Residue 147: PRO, Nonterminal, was not found in name map.) (Residue 148: GLY, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: MET, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: PRO, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: PHE, Nonterminal, was not found in name map.) (Residue 156: LEU, Nonterminal, was not found in name map.) (Residue 157: ASN, Nonterminal, was not found in name map.) (Residue 158: ASP, Nonterminal, was not found in name map.) (Residue 159: SER, Nonterminal, was not found in name map.) (Residue 160: THR, Nonterminal, was not found in name map.) (Residue 161: SER, Nonterminal, was not found in name map.) (Residue 162: SER, Nonterminal, was not found in name map.) (Residue 163: LEU, Nonterminal, was not found in name map.) (Residue 164: TYR, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: SER, Nonterminal, was not found in name map.) (Residue 167: ASN, Nonterminal, was not found in name map.) (Residue 168: ARG, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: GLN, Nonterminal, was not found in name map.) (Residue 171: SER, Nonterminal, was not found in name map.) (Residue 172: HIE, Nonterminal, was not found in name map.) (Residue 173: LEU, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PRO, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: VAL, Nonterminal, was not found in name map.) (Residue 178: VAL, Nonterminal, was not found in name map.) (Residue 179: ASP, Nonterminal, was not found in name map.) (Residue 180: LEU, Nonterminal, was not found in name map.) (Residue 181: GLY, Nonterminal, was not found in name map.) (Residue 182: TYR, Nonterminal, was not found in name map.) (Residue 183: ASN, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: ALA, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: THR, Nonterminal, was not found in name map.) (Residue 188: ASP, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: THR, Nonterminal, was not found in name map.) (Residue 191: ASP, Nonterminal, was not found in name map.) (Residue 192: GLN, Nonterminal, was not found in name map.) (Residue 193: GLN, Nonterminal, was not found in name map.) (Residue 194: ARG, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: ASP, Nonterminal, was not found in name map.) (Residue 198: ASN, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: ALA, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: MET, Nonterminal, was not found in name map.) (Residue 203: TYR, Nonterminal, was not found in name map.) (Residue 204: LYS, Nonterminal, was not found in name map.) (Residue 205: GLN, Nonterminal, was not found in name map.) (Residue 206: MET, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ALA, Nonterminal, was not found in name map.) (Residue 211: GLY, Nonterminal, was not found in name map.) (Residue 212: THR, Nonterminal, was not found in name map.) (Residue 213: ALA, Nonterminal, was not found in name map.) (Residue 214: GLU, Nonterminal, was not found in name map.) (Residue 215: LEU, Nonterminal, was not found in name map.) (Residue 216: PHE, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: LYS, Nonterminal, was not found in name map.) (Residue 220: ALA, Nonterminal, was not found in name map.) (Residue 221: TYR, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: ALA, Nonterminal, was not found in name map.) (Residue 224: GLY, Nonterminal, was not found in name map.) (Residue 225: ASP, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: PRO, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: PRO, Nonterminal, was not found in name map.) (Residue 230: GLY, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLY, Nonterminal, was not found in name map.) (Residue 233: SER, Nonterminal, was not found in name map.) (Residue 234: ILE, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: SER, Nonterminal, was not found in name map.) (Residue 238: PRO, Nonterminal, was not found in name map.) (Residue 239: HID, Nonterminal, was not found in name map.) (Residue 240: ILE, Nonterminal, was not found in name map.) (Residue 241: PRO, Nonterminal, was not found in name map.) (Residue 242: ILE, Nonterminal, was not found in name map.) (Residue 243: HID, Nonterminal, was not found in name map.) (Residue 244: ARG, Nonterminal, was not found in name map.) (Residue 245: TRP, Nonterminal, was not found in name map.) (Residue 246: VAL, Nonterminal, was not found in name map.) (Residue 247: GLY, Nonterminal, was not found in name map.) (Residue 248: ASP, Nonterminal, was not found in name map.) (Residue 249: PRO, Nonterminal, was not found in name map.) (Residue 250: ARG, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: THR, Nonterminal, was not found in name map.) (Residue 253: ASN, Nonterminal, was not found in name map.) (Residue 254: ASN, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: ASP, Nonterminal, was not found in name map.) (Residue 257: MET, Nonterminal, was not found in name map.) (Residue 258: GLY, Nonterminal, was not found in name map.) (Residue 259: ASN, Nonterminal, was not found in name map.) (Residue 260: PHE, Nonterminal, was not found in name map.) (Residue 261: TYR, Nonterminal, was not found in name map.) (Residue 262: SER, Nonterminal, was not found in name map.) (Residue 263: ALA, Nonterminal, was not found in name map.) (Residue 264: GLY, Nonterminal, was not found in name map.) (Residue 265: ARG, Nonterminal, was not found in name map.) (Residue 266: ASP, Nonterminal, was not found in name map.) (Residue 267: ILE, Nonterminal, was not found in name map.) (Residue 268: ALA, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: TYR, Nonterminal, was not found in name map.) (Residue 271: CYS, Nonterminal, was not found in name map.) (Residue 272: HIE, Nonterminal, was not found in name map.) (Residue 273: HID, Nonterminal, was not found in name map.) (Residue 274: SER, Nonterminal, was not found in name map.) (Residue 275: ASN, Nonterminal, was not found in name map.) (Residue 276: VAL, Nonterminal, was not found in name map.) (Residue 277: ASP, Nonterminal, was not found in name map.) (Residue 278: ARG, Nonterminal, was not found in name map.) (Residue 279: MET, Nonterminal, was not found in name map.) (Residue 280: TRP, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: ILE, Nonterminal, was not found in name map.) (Residue 283: TRP, Nonterminal, was not found in name map.) (Residue 284: GLN, Nonterminal, was not found in name map.) (Residue 285: GLN, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: ALA, Nonterminal, was not found in name map.) (Residue 288: GLY, Nonterminal, was not found in name map.) (Residue 289: LYS, Nonterminal, was not found in name map.) (Residue 290: ARG, Nonterminal, was not found in name map.) (Residue 291: ARG, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: TYR, Nonterminal, was not found in name map.) (Residue 294: THR, Nonterminal, was not found in name map.) (Residue 295: ASP, Nonterminal, was not found in name map.) (Residue 296: SER, Nonterminal, was not found in name map.) (Residue 297: ASP, Nonterminal, was not found in name map.) (Residue 298: TRP, Nonterminal, was not found in name map.) (Residue 299: LEU, Nonterminal, was not found in name map.) (Residue 300: ASN, Nonterminal, was not found in name map.) (Residue 301: ALA, Nonterminal, was not found in name map.) (Residue 302: THR, Nonterminal, was not found in name map.) (Residue 303: PHE, Nonterminal, was not found in name map.) (Residue 304: LEU, Nonterminal, was not found in name map.) (Residue 305: PHE, Nonterminal, was not found in name map.) (Residue 306: TYR, Nonterminal, was not found in name map.) (Residue 307: ASP, Nonterminal, was not found in name map.) (Residue 308: GLU, Nonterminal, was not found in name map.) (Residue 309: ASN, Nonterminal, was not found in name map.) (Residue 310: GLY, Nonterminal, was not found in name map.) (Residue 311: GLN, Nonterminal, was not found in name map.) (Residue 312: ALA, Nonterminal, was not found in name map.) (Residue 313: VAL, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: VAL, Nonterminal, was not found in name map.) (Residue 316: ARG, Nonterminal, was not found in name map.) (Residue 317: ILE, Nonterminal, was not found in name map.) (Residue 318: GLY, Nonterminal, was not found in name map.) (Residue 319: ASP, Nonterminal, was not found in name map.) (Residue 320: SER, Nonterminal, was not found in name map.) (Residue 321: LEU, Nonterminal, was not found in name map.) (Residue 322: ASP, Nonterminal, was not found in name map.) (Residue 323: ASN, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: LYS, Nonterminal, was not found in name map.) (Residue 326: MET, Nonterminal, was not found in name map.) (Residue 327: GLY, Nonterminal, was not found in name map.) (Residue 328: TYR, Nonterminal, was not found in name map.) (Residue 329: LYS, Nonterminal, was not found in name map.) (Residue 330: TYR, Nonterminal, was not found in name map.) (Residue 331: ALA, Nonterminal, was not found in name map.) (Residue 332: LYS, Nonterminal, was not found in name map.) (Residue 333: THR, Nonterminal, was not found in name map.) (Residue 334: PRO, Nonterminal, was not found in name map.) (Residue 335: LEU, Nonterminal, was not found in name map.) (Residue 336: PRO, Nonterminal, was not found in name map.) (Residue 337: TRP, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: NHE, Terminal/last, was not found in name map.) (Residue 340: MOL, Terminal/last, was not found in name map.) (Residue 341: MOL, Terminal/last, was not found in name map.) (Residue 342: O2, Terminal/last, was not found in name map.) (Residue 343: O2, Terminal/last, was not found in name map.) Joining ACE - PRO Joining PRO - ILE Joining ILE - GLN Joining GLN - ALA Joining ALA - PRO Joining PRO - GLU Joining GLU - ILE Joining ILE - SER Joining SER - LYS Joining LYS - CYX Joining CYX - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - PRO Joining PRO - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - ASN Joining ASN - CYX Joining CYX - CYX Joining CYX - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - ALA Joining ALA - SER Joining SER - ASN Joining ASN - ILE Joining ILE - VAL Joining VAL - ASP Joining ASP - TYR Joining TYR - LYS Joining LYS - LEU Joining LEU - PRO Joining PRO - ALA Joining ALA - VAL Joining VAL - THR Joining THR - THR Joining THR - MET Joining MET - LYS Joining LYS - VAL Joining VAL - ARG Joining ARG - PRO Joining PRO - ALA Joining ALA - ALA Joining ALA - HIE Joining HIE - THR Joining THR - MET Joining MET - ASP Joining ASP - LYS Joining LYS - ASP Joining ASP - ALA Joining ALA - ILE Joining ILE - ALA Joining ALA - LYS Joining LYS - PHE Joining PHE - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - MET Joining MET - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - PRO Joining PRO - ALA Joining ALA - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - PHE Joining PHE - TYR Joining TYR - GLN Joining GLN - GLN Joining GLN - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - HID Joining HID - CYX Joining CYX - ALA Joining ALA - TYR Joining TYR - CYD Joining CYD - ASN Joining ASN - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - ASP Joining ASP - GLN Joining GLN - VAL Joining VAL - ASN Joining ASN - PHE Joining PHE - PRO Joining PRO - ASP Joining ASP - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - GLN Joining GLN - VAL Joining VAL - HIT Joining HIT - ASN Joining ASN - SER Joining SER - TRP Joining TRP - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - HID Joining HID - ARG Joining ARG - TRP Joining TRP - TYR Joining TYR - LEU Joining LEU - TYR Joining TYR - PHE Joining PHE - TYR Joining TYR - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - ASP Joining ASP - PRO Joining PRO - SER Joining SER - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - TRP Joining TRP - ASN Joining ASN - TRP Joining TRP - ASP Joining ASP - ASN Joining ASN - PRO Joining PRO - GLY Joining GLY - GLY Joining GLY - MET Joining MET - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASN Joining ASN - ASP Joining ASP - SER Joining SER - THR Joining THR - SER Joining SER - SER Joining SER - LEU Joining LEU - TYR Joining TYR - ASP Joining ASP - SER Joining SER - ASN Joining ASN - ARG Joining ARG - ASN Joining ASN - GLN Joining GLN - SER Joining SER - HIE Joining HIE - LEU Joining LEU - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - LEU Joining LEU - GLY Joining GLY - TYR Joining TYR - ASN Joining ASN - GLY Joining GLY - ALA Joining ALA - ASP Joining ASP - THR Joining THR - ASP Joining ASP - VAL Joining VAL - THR Joining THR - ASP Joining ASP - GLN Joining GLN - GLN Joining GLN - ARG Joining ARG - ILE Joining ILE - THR Joining THR - ASP Joining ASP - ASN Joining ASN - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - MET Joining MET - TYR Joining TYR - LYS Joining LYS - GLN Joining GLN - MET Joining MET - VAL Joining VAL - THR Joining THR - ASN Joining ASN - ALA Joining ALA - GLY Joining GLY - THR Joining THR - ALA Joining ALA - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - ALA Joining ALA - TYR Joining TYR - ARG Joining ARG - ALA Joining ALA - GLY Joining GLY - ASP Joining ASP - ALA Joining ALA - PRO Joining PRO - SER Joining SER - PRO Joining PRO - GLY Joining GLY - ALA Joining ALA - GLY Joining GLY - SER Joining SER - ILE Joining ILE - GLU Joining GLU - THR Joining THR - SER Joining SER - PRO Joining PRO - HID Joining HID - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - HID Joining HID - ARG Joining ARG - TRP Joining TRP - VAL Joining VAL - GLY Joining GLY - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - THR Joining THR - ASN Joining ASN - ASN Joining ASN - GLU Joining GLU - ASP Joining ASP - MET Joining MET - GLY Joining GLY - ASN Joining ASN - PHE Joining PHE - TYR Joining TYR - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - ALA Joining ALA - PHE Joining PHE - TYR Joining TYR - CYS Joining CYS - HIE Joining HIE - HID Joining HID - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - MET Joining MET - TRP Joining TRP - THR Joining THR - ILE Joining ILE - TRP Joining TRP - GLN Joining GLN - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - ARG Joining ARG - ASP Joining ASP - TYR Joining TYR - THR Joining THR - ASP Joining ASP - SER Joining SER - ASP Joining ASP - TRP Joining TRP - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - THR Joining THR - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - GLN Joining GLN - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - ARG Joining ARG - ILE Joining ILE - GLY Joining GLY - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - GLN Joining GLN - LYS Joining LYS - MET Joining MET - GLY Joining GLY - TYR Joining TYR - LYS Joining LYS - TYR Joining TYR - ALA Joining ALA - LYS Joining LYS - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - TRP Joining TRP - LEU Joining LEU - NHE total atoms in file: 5245 > bond x.92.SG x.109.CE1 > bond x.341.CUP x.109.NE2 > bond x.27.SG x.89.SG > bond x.28.SG x.11.SG > bond x.343.Omu2 x.344.Omu2 > bond x.341.CUP x.343.Omu2 > bond x.342.CUP x.344.Omu2 > bond x.342.CUP x.240.NE2 > check x Checking 'x'.... WARNING: There is a bond of 3.416120 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.078862 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -7.000000 is not zero. Warning: Close contact of 1.166232 angstroms between .R.A and .R.A Warning: Close contact of 0.970081 angstroms between .R.A and .R.A Warning: Close contact of 1.333642 angstroms between .R.A and .R.A Warning: Close contact of 1.235172 angstroms between .R.A and .R.A Warning: Close contact of 1.456402 angstroms between .R.A and .R.A Warning: Close contact of 1.224178 angstroms between .R.A and .R.A Warning: Close contact of 1.089698 angstroms between .R.A and .R.A Warning: Close contact of 1.090324 angstroms between .R.A and .R.A Warning: Close contact of 1.090030 angstroms between .R.A and .R.A Warning: Close contact of 1.455549 angstroms between .R.A and .R.A Warning: Close contact of 1.009639 angstroms between .R.A and .R.A Warning: Close contact of 1.222278 angstroms between .R.A and .R.A Warning: Close contact of 1.477530 angstroms between .R.A and .R.A Warning: Close contact of 1.090197 angstroms between .R.A and .R.A Warning: Close contact of 1.009832 angstroms between .R.A and .R.A Warning: Close contact of 1.090033 angstroms between .R.A and .R.A Warning: Close contact of 1.090176 angstroms between .R.A and .R.A Warning: Close contact of 1.089953 angstroms between .R.A and .R.A Warning: Close contact of 1.009929 angstroms between .R.A and .R.A Warning: Close contact of 1.321081 angstroms between .R.A and .R.A Warning: Close contact of 1.372009 angstroms between .R.A and .R.A Warning: Close contact of 1.315167 angstroms between .R.A and .R.A Warning: Close contact of 1.375125 angstroms between .R.A and .R.A Warning: Close contact of 1.349718 angstroms between .R.A and .R.A Warning: Close contact of 1.480385 angstroms between .R.A and .R.A Warning: Close contact of 1.451370 angstroms between .R.A and .R.A Warning: Close contact of 1.160735 angstroms between .R.A and .R.A Warning: Close contact of 1.493268 angstroms between .R.A and .R.A Warning: Close contact of 1.402872 angstroms between .R.A and .R.A Warning: Close contact of 1.477022 angstroms between .R.A and .R.A Warning: Close contact of 1.055926 angstroms between .R.A and .R.A Warning: Close contact of 0.832519 angstroms between .R.A and .R.A Warning: Close contact of 1.485055 angstroms between .R.A and .R.A Warning: Close contact of 0.919875 angstroms between .R.A and .R.A Warning: Close contact of 1.273936 angstroms between .R.A and .R.A Checking parameters for unit 'x'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 38 Unit is OK. > saveamberparm x PPO.prmtop PPO.inpcrd Checking Unit. WARNING: There is a bond of 3.416120 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.078862 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -7.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. ** No torsion terms for na-CU-Omu2-Omu2 ** No torsion terms for NB-CU-Omu2-Omu2 ** No torsion terms for CU-Omu2-Omu2-CU 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 CR-CV-NB-CU atoms are: CE1 CD2 NE2 CUP ** 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 1127 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Parameter file was not saved. > savepdb x protein_tleap_prova.pdb Writing pdb file: protein_tleap_prova.pdb > saveoff x protein_tleap_prova.lib Creating protein_tleap_prova.lib Saving x. Building topology. Building atom parameters. > quit Quit