log started: Thu Jun 16 09:39:12 2005 Log file: ./leap.log > # > # ----- leaprc for loading the parm99 additive force field, no lone pairs > # assumes that any unspecified nucleic acids are DNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/common/amber/amber8/irix/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries. > # > loadOff all_amino94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > > loadOff ions94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > loadamberparams gaff.dat Loading parameters: /usr/common/amber/amber8/irix/amber8/dat/leap/parm/gaff.dat (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > loadamberprep HET.prep Loading Prep file: ./HET.prep (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hn) Loaded UNIT: HET > loadamberparams HET.parm Loading parameters: ./HET.parm Reading force field mod type file (frcmod) > b=loadpdb "foramberaha203.pdb" Loading PDB file: ./foramberaha203.pdb -- residue 15: duplicate [HB3] atoms (total 2) -- residue 21: duplicate [HB3] atoms (total 2) -- residue 46: duplicate [HA3] atoms (total 2) -- residue 76: duplicate [HB3] atoms (total 2) -- residue 82: duplicate [HB3] atoms (total 2) -- residue 107: duplicate [HA3] atoms (total 2) -- residue 131: duplicate [C] atoms (total 54) -- residue 131: duplicate [H] atoms (total 44) -- residue 131: duplicate [H1] atoms (total 4) -- residue 131: duplicate [H2] atoms (total 4) -- residue 131: duplicate [N] atoms (total 2) -- residue 131: duplicate [O] atoms (total 8) ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE: (same-name atoms are reduced to a single atom) Matching PDB residue names to LEaP variables. Mapped residue THR, term: Terminal/beginning, seq. number: 0 to: NTHR. (Residue 1: LEU, Nonterminal, was not found in name map.) (Residue 2: TRP, Nonterminal, was not found in name map.) (Residue 3: GLN, Nonterminal, was not found in name map.) (Residue 4: ARG, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: VAL, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 8 to: CTHR. Mapped residue LYS, term: Terminal/beginning, seq. number: 9 to: NLYS. (Residue 10: GLU, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: THR, Nonterminal, was not found in name map.) (Residue 16: GLY, Nonterminal, was not found in name map.) (Residue 17: ALA, Nonterminal, was not found in name map.) (Residue 18: ASP, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: VAL, Nonterminal, was not found in name map.) (Residue 22: LEU, Nonterminal, was not found in name map.) (Residue 23: GLU, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 24 to: CGLU. Mapped residue PRO, term: Terminal/beginning, seq. number: 25 to: NPRO. (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: MET, Nonterminal, was not found in name map.) (Residue 28: ILE, Nonterminal, was not found in name map.) (Residue 29: GLY, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: ILE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: PHE, Nonterminal, was not found in name map.) (Residue 35: ILE, Nonterminal, was not found in name map.) (Residue 36: LYS, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: ARG, Nonterminal, was not found in name map.) (Residue 39: GLN, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 41 to: CASP. Mapped residue GLY, term: Terminal/beginning, seq. number: 42 to: NGLY. (Residue 43: THR, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: LEU, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: PRO, Nonterminal, was not found in name map.) (Residue 49: THR, Nonterminal, was not found in name map.) (Residue 50: PRO, Nonterminal, was not found in name map.) (Residue 51: VAL, Nonterminal, was not found in name map.) (Residue 52: ASN, Nonterminal, was not found in name map.) (Residue 53: ILE, Nonterminal, was not found in name map.) (Residue 54: ILE, Nonterminal, was not found in name map.) (Residue 55: GLY, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: ASN, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: LEU, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 60 to: CTHR. Mapped residue THR, term: Terminal/beginning, seq. number: 61 to: NTHR. (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: TRP, Nonterminal, was not found in name map.) (Residue 64: GLN, Nonterminal, was not found in name map.) (Residue 65: ARG, Nonterminal, was not found in name map.) (Residue 66: PRO, Nonterminal, was not found in name map.) (Residue 67: LEU, Nonterminal, was not found in name map.) (Residue 68: VAL, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 69 to: CTHR. Mapped residue LYS, term: Terminal/beginning, seq. number: 70 to: NLYS. (Residue 71: GLU, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: LEU, Nonterminal, was not found in name map.) (Residue 74: LEU, Nonterminal, was not found in name map.) (Residue 75: ASP, Nonterminal, was not found in name map.) (Residue 76: THR, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: ALA, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: ASP, Nonterminal, was not found in name map.) (Residue 81: THR, Nonterminal, was not found in name map.) (Residue 82: VAL, Nonterminal, was not found in name map.) (Residue 83: LEU, Nonterminal, was not found in name map.) (Residue 84: GLU, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 85 to: CGLU. Mapped residue PRO, term: Terminal/beginning, seq. number: 86 to: NPRO. (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: MET, Nonterminal, was not found in name map.) (Residue 89: ILE, Nonterminal, was not found in name map.) (Residue 90: GLY, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: ILE, 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: PHE, Nonterminal, was not found in name map.) (Residue 96: ILE, Nonterminal, was not found in name map.) (Residue 97: LYS, Nonterminal, was not found in name map.) (Residue 98: VAL, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: GLN, Nonterminal, was not found in name map.) (Residue 101: TYR, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 102 to: CASP. Mapped residue GLY, term: Terminal/beginning, seq. number: 103 to: NGLY. (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: VAL, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: VAL, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: PRO, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: VAL, Nonterminal, was not found in name map.) (Residue 113: ASN, Nonterminal, was not found in name map.) (Residue 114: ILE, Nonterminal, was not found in name map.) (Residue 115: ILE, Nonterminal, was not found in name map.) (Residue 116: GLY, Nonterminal, was not found in name map.) (Residue 117: ARG, Nonterminal, was not found in name map.) (Residue 118: ASN, Nonterminal, was not found in name map.) (Residue 119: LEU, Nonterminal, was not found in name map.) (Residue 120: LEU, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 121 to: CTHR. (Residue 122: HET, Terminal/beginning, was not found in name map.) (Residue 123: HET, Nonterminal, was not found in name map.) (Residue 124: HET, Nonterminal, was not found in name map.) (Residue 125: HET, Nonterminal, was not found in name map.) (Residue 126: HET, Nonterminal, was not found in name map.) (Residue 127: HET, Terminal/last, was not found in name map.) Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NTHR - LEU Created a new atom named: HN within residue: .R Joining LEU - TRP Created a new atom named: HNE within residue: .R Created a new atom named: HD within residue: .R Created a new atom named: HZ1 within residue: .R Created a new atom named: HH within residue: .R Created a new atom named: HE within residue: .R Created a new atom named: HN within residue: .R Joining TRP - GLN Created a new atom named: HNE2 within residue: .R Created a new atom named: HNE1 within residue: .R Created a new atom named: HN within residue: .R Joining GLN - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - PRO Joining PRO - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - CTHR Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NLYS - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ASP Created a new atom named: HD2 within residue: .R Created a new atom named: HN within residue: .R Joining ASP - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASP Created a new atom named: HN within residue: .R Joining ASP - ASP Created a new atom named: HN within residue: .R Joining ASP - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - GLU Created a new atom named: HN within residue: .R Joining GLU - CGLU Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NPRO - LYS Created a new atom named: HNZ1 within residue: .R Created a new atom named: HNZ2 within residue: .R Created a new atom named: HNZ3 within residue: .R Created a new atom named: HN within residue: .R Joining LYS - MET Created a new atom named: HN within residue: .R Joining MET - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HNZ1 within residue: .R Created a new atom named: HNZ2 within residue: .R Created a new atom named: HNZ3 within residue: .R Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - GLN Created a new atom named: HNE2 within residue: .R Created a new atom named: HNE1 within residue: .R Created a new atom named: HN within residue: .R Joining GLN - TYR Created a new atom named: HOH within residue: .R Created a new atom named: HN within residue: .R Joining TYR - CASP Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NGLY - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - PRO Joining PRO - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - ASN Created a new atom named: HND2 within residue: .R Created a new atom named: HND1 within residue: .R Created a new atom named: HN within residue: .R Joining ASN - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HND2 within residue: .R Created a new atom named: HND1 within residue: .R Created a new atom named: HN within residue: .R Joining ASN - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - CTHR Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NTHR - LEU Created a new atom named: HN within residue: .R Joining LEU - TRP Created a new atom named: HNE within residue: .R Created a new atom named: HD within residue: .R Created a new atom named: HZ1 within residue: .R Created a new atom named: HH within residue: .R Created a new atom named: HE within residue: .R Created a new atom named: HN within residue: .R Joining TRP - GLN Created a new atom named: HNE2 within residue: .R Created a new atom named: HNE1 within residue: .R Created a new atom named: HN within residue: .R Joining GLN - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - PRO Joining PRO - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - CTHR Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NLYS - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ASP Created a new atom named: HD2 within residue: .R Created a new atom named: HN within residue: .R Joining ASP - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASP Created a new atom named: HN within residue: .R Joining ASP - ASP Created a new atom named: HN within residue: .R Joining ASP - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - GLU Created a new atom named: HN within residue: .R Joining GLU - CGLU Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NPRO - LYS Created a new atom named: HNZ1 within residue: .R Created a new atom named: HNZ2 within residue: .R Created a new atom named: HNZ3 within residue: .R Created a new atom named: HN within residue: .R Joining LYS - MET Created a new atom named: HN within residue: .R Joining MET - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HNZ1 within residue: .R Created a new atom named: HNZ2 within residue: .R Created a new atom named: HNZ3 within residue: .R Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - GLN Created a new atom named: HNE2 within residue: .R Created a new atom named: HNE1 within residue: .R Created a new atom named: HN within residue: .R Joining GLN - TYR Created a new atom named: HOH within residue: .R Created a new atom named: HN within residue: .R Joining TYR - CASP Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NGLY - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - PRO Joining PRO - THR Created a new atom named: HOG within residue: .R Created a new atom named: HG3 within residue: .R Created a new atom named: HG2 within residue: .R Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - ASN Created a new atom named: HND2 within residue: .R Created a new atom named: HND1 within residue: .R Created a new atom named: HN within residue: .R Joining ASN - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - ILE Created a new atom named: HD1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HD3 within residue: .R Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - ARG Created a new atom named: HNE within residue: .R Created a new atom named: HN12 within residue: .R Created a new atom named: HN11 within residue: .R Created a new atom named: HN22 within residue: .R Created a new atom named: HN21 within residue: .R Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HND2 within residue: .R Created a new atom named: HND1 within residue: .R Created a new atom named: HN within residue: .R Joining ASN - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - CTHR Created a new atom named: HA3 within residue: .R Created a new atom named: HA2 within residue: .R Created a new atom named: HA1 within residue: .R Created a new atom named: HN within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining HET - HET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining HET - HET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining HET - HET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining HET - HET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining HET - HET Bond: maximum coordination exceeded on .R.A -- setting atoms pert=true overrides default limits ATOMS NOT BONDED: .R.A .R.A log started: Thu Jun 16 09:42:34 2005 Log file: ./leap.log > # > # ----- leaprc for loading the parm99 additive force field, no lone pairs > # assumes that any unspecified nucleic acids are DNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/common/amber/amber8/irix/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries. > # > loadOff all_amino94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > > loadOff ions94.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /usr/common/amber/amber8/irix/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > loadamberparams gaff.dat Loading parameters: /usr/common/amber/amber8/irix/amber8/dat/leap/parm/gaff.dat (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > loadamberprep HET.prep Loading Prep file: ./HET.prep (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hn) Loaded UNIT: HET > loadamberparams HET.parm Loading parameters: ./HET.parm Reading force field mod type file (frcmod) > quit Quit