log started: Sat Oct 13 17:54:04 2018 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" } >> { "cs" "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" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "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" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "N" "sp3" } >> { "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 gaff2.dat Loading parameters: /home/senal-research/amber16/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.1, April 2016) > > source leaprc.protein.ff14SB ----- Source: /home/senal-research/amber16/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/senal-research/amber16/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Sat Oct 13 17:54:04 2018 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # 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" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/senal-research/amber16/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/senal-research/amber16/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 >> # >> loadOff amino12.lib Loading library: /home/senal-research/amber16/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/senal-research/amber16/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/senal-research/amber16/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 >> >> # >> # Define the PDB name map for the amino 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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.GLYCAM_06j-1 ----- Source: /home/senal-research/amber16/dat/leap/cmd/leaprc.GLYCAM_06j-1 ----- Source of /home/senal-research/amber16/dat/leap/cmd/leaprc.GLYCAM_06j-1 done >> # ----- leaprc for loading the Glycam_06 carbohydrate force field >> # also contains atom types for lipids >> # >> # load atom type hybridizations >> # (includes atom types relevant to lipids) >> # >> addAtomTypes { >> { "C" "C" "sp2" } >> { "Cg" "C" "sp3" } >> { "Cy" "C" "sp3" } >> { "Ck" "C" "sp2" } >> { "CT" "C" "sp3" } >> { "Cj" "C" "sp2" } >> { "Cp" "C" "sp3" } >> { "H" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "Ha" "H" "sp3" } >> { "Hp" "H" "sp3" } >> { "Hc" "H" "sp3" } >> { "Ho" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "Ng" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "Oh" "O" "sp3" } >> { "Os" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "Oy" "O" "sp3" } >> { "S" "S" "sp3" } >> { "Sm" "S" "sp3" } >> { "P" "P" "sp3" } >> } >> # >> # load the main paramter set >> # >> glycam_06 = loadamberparams GLYCAM_06j.dat Loading parameters: /home/senal-research/amber16/dat/leap/parm/GLYCAM_06j.dat Reading title: GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011 >> ## >> # >> # load all prep files for polysaccharides >> # >> loadamberprep GLYCAM_06j-1.prep Loading Prep file: /home/senal-research/amber16/dat/leap/prep/GLYCAM_06j-1.prep Loaded UNIT: 0AA Loaded UNIT: 0AB Loaded 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Loaded UNIT: XnB Loaded UNIT: XtA Loaded UNIT: XtB Loaded UNIT: YAA Loaded UNIT: YAB Loaded UNIT: YAF Loaded UNIT: YDA Loaded UNIT: YDB Loaded UNIT: YEA Loaded UNIT: YEB Loaded UNIT: YFA Loaded UNIT: YFB Loaded UNIT: YGA Loaded UNIT: YGB Loaded UNIT: YGa Loaded UNIT: YHA Loaded UNIT: YHB Loaded UNIT: YKA Loaded UNIT: YKB Loaded UNIT: YLA Loaded UNIT: YLB Loaded UNIT: YMA Loaded UNIT: YMB Loaded UNIT: YNA Loaded UNIT: YNB Loaded UNIT: YOA Loaded UNIT: YOB Loaded UNIT: YQA Loaded UNIT: YQB Loaded UNIT: YRA Loaded UNIT: YRB Loaded UNIT: YTA Loaded UNIT: YTB Loaded UNIT: YTV Loaded UNIT: YTv Loaded UNIT: YUA Loaded UNIT: YUB Loaded UNIT: YXA Loaded UNIT: YXB Loaded UNIT: YZA Loaded UNIT: YZB Loaded UNIT: YaA Loaded UNIT: YaB Loaded UNIT: YdA Loaded UNIT: YdB Loaded UNIT: YeA Loaded UNIT: YeB Loaded UNIT: YfA Loaded UNIT: YfB Loaded UNIT: YgA Loaded UNIT: YgB Loaded UNIT: YhA Loaded UNIT: YhB Loaded UNIT: YkA Loaded UNIT: YkB Loaded UNIT: YlA Loaded UNIT: YlB Loaded UNIT: YmA Loaded UNIT: YmB Loaded UNIT: YnA Loaded UNIT: YnB Loaded UNIT: YoA Loaded UNIT: YoB Loaded UNIT: YqA Loaded UNIT: YqB Loaded UNIT: YrA Loaded UNIT: YrB Loaded UNIT: YtA Loaded UNIT: YtB Loaded UNIT: YtV Loaded UNIT: Ytv Loaded UNIT: YuA Loaded UNIT: YuB Loaded UNIT: YxA Loaded UNIT: YxB Loaded UNIT: YzA Loaded UNIT: YzB Loaded UNIT: ZAA Loaded UNIT: ZAB Loaded UNIT: ZAD Loaded UNIT: ZAU Loaded UNIT: ZDA Loaded UNIT: ZDB Loaded UNIT: ZDD Loaded UNIT: ZDU Loaded UNIT: ZEA Loaded UNIT: ZEB Loaded UNIT: ZFA Loaded UNIT: ZFB Loaded UNIT: ZGA Loaded UNIT: ZGB Loaded UNIT: ZHA Loaded UNIT: ZHB Loaded UNIT: ZKA Loaded UNIT: ZKB Loaded UNIT: ZLA Loaded UNIT: ZLB Loaded UNIT: ZMA Loaded UNIT: ZMB Loaded UNIT: ZNA Loaded UNIT: ZNB Loaded UNIT: ZOA Loaded UNIT: ZOB Loaded UNIT: ZOLS Loaded UNIT: ZOLT Loaded UNIT: ZQA Loaded UNIT: ZQB Loaded UNIT: ZRA Loaded UNIT: ZRB Loaded UNIT: ZRD Loaded UNIT: ZRU Loaded UNIT: ZTA Loaded UNIT: ZTB Loaded UNIT: ZUA Loaded UNIT: ZUB Loaded UNIT: ZXA Loaded UNIT: ZXB Loaded UNIT: ZXD Loaded UNIT: ZXU Loaded UNIT: ZZA Loaded UNIT: ZZB Loaded UNIT: ZaA Loaded UNIT: ZaB Loaded UNIT: ZaD Loaded UNIT: ZaU Loaded UNIT: ZdA Loaded UNIT: ZdB Loaded UNIT: ZdD Loaded UNIT: ZdU Loaded UNIT: ZeA Loaded UNIT: ZeB Loaded UNIT: ZfA Loaded UNIT: ZfB Loaded UNIT: ZgA Loaded UNIT: ZgB Loaded UNIT: ZhA Loaded UNIT: ZhB Loaded UNIT: ZkA Loaded UNIT: ZkB Loaded UNIT: ZlA Loaded UNIT: ZlB Loaded UNIT: ZmA Loaded UNIT: ZmB Loaded UNIT: ZnA Loaded UNIT: ZnB Loaded UNIT: ZoA Loaded UNIT: ZoB Loaded UNIT: ZqA Loaded UNIT: ZqB Loaded UNIT: ZrA Loaded UNIT: ZrB Loaded UNIT: ZrD Loaded UNIT: ZrU Loaded UNIT: ZtA Loaded UNIT: ZtB Loaded UNIT: ZuA Loaded UNIT: ZuB Loaded UNIT: ZxA Loaded UNIT: ZxB Loaded UNIT: ZxD Loaded UNIT: ZxU Loaded UNIT: ZzA Loaded UNIT: ZzB >> # >> # load lib files >> # >> # for attaching glycans to proteins >> loadOff GLYCAM_amino_06j_12SB.lib Loading library: /home/senal-research/amber16/dat/leap/lib/GLYCAM_amino_06j_12SB.lib Loading: HYP Loading: NLN Loading: OLP Loading: OLS Loading: OLT >> loadOff GLYCAM_aminoct_06j_12SB.lib Loading library: /home/senal-research/amber16/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib Loading: CHYP Loading: CNLN Loading: COLP Loading: COLS Loading: COLT >> loadOff GLYCAM_aminont_06j_12SB.lib Loading library: /home/senal-research/amber16/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib Loading: NHYP Loading: NNLN Loading: NOLP Loading: NOLS Loading: NOLT >> ## add residue maps for linking glycans to proteins >> ## Note! use of these requires sourcing the ff12SB leaprc and loading the amino >> ## libraries commented out in the load libs section >> addPdbResMap { >> { 0 "OLS" "NOLS" } { 1 "OLS" "COLS" } >> { 0 "OLT" "NOLT" } { 1 "OLT" "COLT" } >> { 0 "OLP" "NOLP" } { 1 "OLP" "COLP" } >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "NLN" "NNLN" } { 1 "NLN" "CNLN" } >> } Substituting map 0HYP -> NHYP for 0HYP -> NHYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP >> # >> # for explicit solvent and ions >> # >> # the following assumes most users want to use tip3p as the >> # explicit solvent model >> # this can easily switched by the following commands in leap: >> # WAT = TP5 >> # loadamberparams frcmod.tip5p >> # >> loadOff solvents.lib # solvents Loading library: /home/senal-research/amber16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX 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 # set default water model >> WAT = TP3 >> loadOff atomic_ions.lib # load ions library Loading library: /home/senal-research/amber16/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 >> # to use ions for TIP5P, you will need to use a different frcmod below >> # If desired, see the AMBER manual for additional ion force field options. >> ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P Loading parameters: ./frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) (UNKNOWN ATOM TYPE: Li+) (UNKNOWN ATOM TYPE: Na+) (UNKNOWN ATOM TYPE: K+) (UNKNOWN ATOM TYPE: Rb+) (UNKNOWN ATOM TYPE: Cs+) (UNKNOWN ATOM TYPE: F-) (UNKNOWN ATOM TYPE: Cl-) (UNKNOWN ATOM TYPE: Br-) (UNKNOWN ATOM TYPE: I-) > > #source leaprc.water.tip3p > #loadamberparams frcmod.ionsjc_tip3p > #loadamberparams frcmod.ions1lm_126_tip3p > loadamberparams l1-lig.frcmod Loading parameters: ./l1-lig.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > bglu1 = loadPdb "l1-prep.pdb" Loading PDB file: ./l1-prep.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: PHE, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: ALA, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: TRP, Nonterminal, was not found in name map.) (Residue 9: ALA, Nonterminal, was not found in name map.) (Residue 10: ALA, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: THR, Nonterminal, was not found in name map.) (Residue 13: ALA, Nonterminal, was not found in name map.) (Residue 14: ALA, Nonterminal, was not found in name map.) (Residue 15: TYR, Nonterminal, was not found in name map.) (Residue 16: GLN, Nonterminal, was not found in name map.) (Residue 17: VAL, Nonterminal, was not found in name map.) (Residue 18: GLU, Nonterminal, was not found in name map.) (Residue 19: GLY, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: TRP, Nonterminal, was not found in name map.) (Residue 22: ASP, Nonterminal, was not found in name map.) (Residue 23: ALA, Nonterminal, was not found in name map.) (Residue 24: ASP, Nonterminal, was not found in name map.) (Residue 25: GLY, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: PRO, Nonterminal, was not found in name map.) (Residue 29: CYS, Nonterminal, was not found in name map.) (Residue 30: VAL, Nonterminal, was not found in name map.) (Residue 31: TRP, Nonterminal, was not found in name map.) (Residue 32: ASP, Nonterminal, was not found in name map.) (Residue 33: THR, Nonterminal, was not found in name map.) (Residue 34: PHE, Nonterminal, was not found in name map.) (Residue 35: THR, Nonterminal, was not found in name map.) (Residue 36: HIP, Nonterminal, was not found in name map.) (Residue 37: GLN, Nonterminal, was not found in name map.) (Residue 38: GLY, Nonterminal, was not found in name map.) (Residue 39: GLY, Nonterminal, was not found in name map.) (Residue 40: GLU, Nonterminal, was not found in name map.) (Residue 41: ARG, Nonterminal, was not found in name map.) (Residue 42: VAL, Nonterminal, was not found in name map.) (Residue 43: PHE, Nonterminal, was not found in name map.) (Residue 44: LYS, Nonterminal, was not found in name map.) (Residue 45: ASN, Nonterminal, was not found in name map.) (Residue 46: GLN, Nonterminal, was not found in name map.) (Residue 47: THR, Nonterminal, was not found in name map.) (Residue 48: GLY, Nonterminal, was not found in name map.) (Residue 49: ASP, Nonterminal, was not found in name map.) (Residue 50: VAL, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: CYS, Nonterminal, was not found in name map.) (Residue 53: GLY, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: TYR, Nonterminal, was not found in name map.) (Residue 56: THR, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: TRP, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: GLU, Nonterminal, was not found in name map.) (Residue 61: ASP, Nonterminal, was not found in name map.) (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: CYS, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: LYS, Nonterminal, was not found in name map.) (Residue 67: GLN, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: LEU, Nonterminal, was not found in name map.) (Residue 71: THR, Nonterminal, was not found in name map.) (Residue 72: HIE, Nonterminal, was not found in name map.) (Residue 73: TYR, Nonterminal, was not found in name map.) (Residue 74: ARG, Nonterminal, was not found in name map.) (Residue 75: PHE, Nonterminal, was not found in name map.) (Residue 76: SER, Nonterminal, was not found in name map.) (Residue 77: LEU, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: TRP, Nonterminal, was not found in name map.) (Residue 80: SER, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: LEU, Nonterminal, was not found in name map.) (Residue 83: LEU, Nonterminal, was not found in name map.) (Residue 84: PRO, Nonterminal, was not found in name map.) (Residue 85: ASP, Nonterminal, was not found in name map.) (Residue 86: GLY, Nonterminal, was not found in name map.) (Residue 87: THR, Nonterminal, was not found in name map.) (Residue 88: THR, Nonterminal, was not found in name map.) (Residue 89: GLY, Nonterminal, was not found in name map.) (Residue 90: PHE, Nonterminal, was not found in name map.) (Residue 91: ILE, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: GLN, Nonterminal, was not found in name map.) (Residue 94: LYS, Nonterminal, was not found in name map.) (Residue 95: GLY, Nonterminal, was not found in name map.) (Residue 96: ILE, Nonterminal, was not found in name map.) (Residue 97: ASP, Nonterminal, was not found in name map.) (Residue 98: TYR, Nonterminal, was not found in name map.) (Residue 99: TYR, Nonterminal, was not found in name map.) (Residue 100: ASN, Nonterminal, was not found in name map.) (Residue 101: LYS, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: ILE, Nonterminal, was not found in name map.) (Residue 104: ASP, Nonterminal, was not found in name map.) (Residue 105: ASP, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: LEU, Nonterminal, was not found in name map.) (Residue 108: LYS, Nonterminal, was not found in name map.) (Residue 109: ASN, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: VAL, Nonterminal, was not found in name map.) (Residue 112: THR, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: ILE, Nonterminal, was not found in name map.) (Residue 115: VAL, Nonterminal, was not found in name map.) (Residue 116: THR, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: TYR, Nonterminal, was not found in name map.) (Residue 119: HIP, Nonterminal, was not found in name map.) (Residue 120: PHE, Nonterminal, was not found in name map.) (Residue 121: ASP, Nonterminal, was not found in name map.) (Residue 122: LEU, Nonterminal, was not found in name map.) (Residue 123: PRO, Nonterminal, was not found in name map.) (Residue 124: GLN, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: ASP, Nonterminal, was not found in name map.) (Residue 129: GLN, Nonterminal, was not found in name map.) (Residue 130: GLY, Nonterminal, was not found in name map.) (Residue 131: GLY, Nonterminal, was not found in name map.) (Residue 132: TRP, Nonterminal, was not found in name map.) (Residue 133: LEU, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: ILE, Nonterminal, was not found in name map.) (Residue 138: ILE, Nonterminal, was not found in name map.) (Residue 139: GLU, Nonterminal, was not found in name map.) (Residue 140: SER, Nonterminal, was not found in name map.) (Residue 141: PHE, Nonterminal, was not found in name map.) (Residue 142: ASP, Nonterminal, was not found in name map.) (Residue 143: LYS, Nonterminal, was not found in name map.) (Residue 144: TYR, Nonterminal, was not found in name map.) (Residue 145: ALA, Nonterminal, was not found in name map.) (Residue 146: GLN, Nonterminal, was not found in name map.) (Residue 147: PHE, Nonterminal, was not found in name map.) (Residue 148: CYS, Nonterminal, was not found in name map.) (Residue 149: PHE, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: THR, Nonterminal, was not found in name map.) (Residue 152: PHE, Nonterminal, was not found in name map.) (Residue 153: GLY, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: ARG, Nonterminal, was not found in name map.) (Residue 156: VAL, Nonterminal, was not found in name map.) (Residue 157: LYS, Nonterminal, was not found in name map.) (Residue 158: GLN, Nonterminal, was not found in name map.) (Residue 159: TRP, Nonterminal, was not found in name map.) (Residue 160: ILE, Nonterminal, was not found in name map.) (Residue 161: THR, Nonterminal, was not found in name map.) (Residue 162: ILE, Nonterminal, was not found in name map.) (Residue 163: ASN, Nonterminal, was not found in name map.) (Residue 164: GLH, Nonterminal, was not found in name map.) (Residue 165: ALA, Nonterminal, was not found in name map.) (Residue 166: ASN, Nonterminal, was not found in name map.) (Residue 167: VAL, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: SER, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: MET, Nonterminal, was not found in name map.) (Residue 172: SER, Nonterminal, was not found in name map.) (Residue 173: TYR, Nonterminal, was not found in name map.) (Residue 174: ASP, Nonterminal, was not found in name map.) (Residue 175: LEU, Nonterminal, was not found in name map.) (Residue 176: GLY, Nonterminal, was not found in name map.) (Residue 177: MET, Nonterminal, was not found in name map.) (Residue 178: PHE, Nonterminal, was not found in name map.) (Residue 179: PRO, Nonterminal, was not found in name map.) (Residue 180: PRO, Nonterminal, was not found in name map.) (Residue 181: GLY, Nonterminal, was not found in name map.) (Residue 182: ILE, Nonterminal, was not found in name map.) (Residue 183: PRO, Nonterminal, was not found in name map.) (Residue 184: HIP, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: GLY, Nonterminal, was not found in name map.) (Residue 187: THR, Nonterminal, was not found in name map.) (Residue 188: GLY, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: TYR, Nonterminal, was not found in name map.) (Residue 191: GLN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: ALA, Nonterminal, was not found in name map.) (Residue 194: HIP, Nonterminal, was not found in name map.) (Residue 195: ASN, Nonterminal, was not found in name map.) (Residue 196: LEU, Nonterminal, was not found in name map.) (Residue 197: ILE, Nonterminal, was not found in name map.) (Residue 198: LYS, Nonterminal, was not found in name map.) (Residue 199: ALA, Nonterminal, was not found in name map.) (Residue 200: HIE, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: ARG, Nonterminal, was not found in name map.) (Residue 203: SER, Nonterminal, was not found in name map.) (Residue 204: TRP, Nonterminal, was not found in name map.) (Residue 205: HIP, Nonterminal, was not found in name map.) (Residue 206: SER, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: ASP, Nonterminal, was not found in name map.) (Residue 209: SER, Nonterminal, was not found in name map.) (Residue 210: LEU, Nonterminal, was not found in name map.) (Residue 211: PHE, Nonterminal, was not found in name map.) (Residue 212: ARG, Nonterminal, was not found in name map.) (Residue 213: LYS, Nonterminal, was not found in name map.) (Residue 214: LYS, Nonterminal, was not found in name map.) (Residue 215: GLN, Nonterminal, was not found in name map.) (Residue 216: LYS, Nonterminal, was not found in name map.) (Residue 217: GLY, Nonterminal, was not found in name map.) (Residue 218: MET, Nonterminal, was not found in name map.) (Residue 219: VAL, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: SER, Nonterminal, was not found in name map.) (Residue 223: LEU, Nonterminal, was not found in name map.) (Residue 224: PHE, Nonterminal, was not found in name map.) (Residue 225: ALA, Nonterminal, was not found in name map.) (Residue 226: VAL, Nonterminal, was not found in name map.) (Residue 227: TRP, Nonterminal, was not found in name map.) (Residue 228: LEU, Nonterminal, was not found in name map.) (Residue 229: GLU, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: ASP, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: ASN, Nonterminal, was not found in name map.) (Residue 235: SER, Nonterminal, was not found in name map.) (Residue 236: VAL, Nonterminal, was not found in name map.) (Residue 237: SER, Nonterminal, was not found in name map.) (Residue 238: ASP, Nonterminal, was not found in name map.) (Residue 239: GLN, Nonterminal, was not found in name map.) (Residue 240: GLU, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: ALA, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: ARG, Nonterminal, was not found in name map.) (Residue 245: ALA, Nonterminal, was not found in name map.) (Residue 246: ILE, Nonterminal, was not found in name map.) (Residue 247: THR, Nonterminal, was not found in name map.) (Residue 248: PHE, Nonterminal, was not found in name map.) (Residue 249: HID, Nonterminal, was not found in name map.) (Residue 250: LEU, Nonterminal, was not found in name map.) (Residue 251: ASP, Nonterminal, was not found in name map.) (Residue 252: LEU, Nonterminal, was not found in name map.) (Residue 253: PHE, Nonterminal, was not found in name map.) (Residue 254: ALA, Nonterminal, was not found in name map.) (Residue 255: LYS, Nonterminal, was not found in name map.) (Residue 256: PRO, Nonterminal, was not found in name map.) (Residue 257: ILE, Nonterminal, was not found in name map.) (Residue 258: PHE, Nonterminal, was not found in name map.) (Residue 259: ILE, Nonterminal, was not found in name map.) (Residue 260: ASP, Nonterminal, was not found in name map.) (Residue 261: GLY, Nonterminal, was not found in name map.) (Residue 262: ASP, Nonterminal, was not found in name map.) (Residue 263: TYR, Nonterminal, was not found in name map.) (Residue 264: PRO, Nonterminal, was not found in name map.) (Residue 265: GLU, Nonterminal, was not found in name map.) (Residue 266: VAL, Nonterminal, was not found in name map.) (Residue 267: VAL, Nonterminal, was not found in name map.) (Residue 268: LYS, Nonterminal, was not found in name map.) (Residue 269: SER, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: ILE, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: SER, Nonterminal, was not found in name map.) (Residue 274: MET, Nonterminal, was not found in name map.) (Residue 275: SER, Nonterminal, was not found in name map.) (Residue 276: GLN, Nonterminal, was not found in name map.) (Residue 277: LYS, Nonterminal, was not found in name map.) (Residue 278: GLN, Nonterminal, was not found in name map.) (Residue 279: GLY, Nonterminal, was not found in name map.) (Residue 280: TYR, Nonterminal, was not found in name map.) (Residue 281: PRO, Nonterminal, was not found in name map.) (Residue 282: SER, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: ARG, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: PRO, Nonterminal, was not found in name map.) (Residue 287: GLU, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: THR, Nonterminal, was not found in name map.) (Residue 290: GLU, Nonterminal, was not found in name map.) (Residue 291: GLU, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LYS, Nonterminal, was not found in name map.) (Residue 294: LYS, Nonterminal, was not found in name map.) (Residue 295: MET, Nonterminal, was not found in name map.) (Residue 296: ILE, Nonterminal, was not found in name map.) (Residue 297: LYS, Nonterminal, was not found in name map.) (Residue 298: GLY, Nonterminal, was not found in name map.) (Residue 299: THR, Nonterminal, was not found in name map.) (Residue 300: ALA, Nonterminal, was not found in name map.) (Residue 301: ASP, Nonterminal, was not found in name map.) (Residue 302: PHE, Nonterminal, was not found in name map.) (Residue 303: PHE, Nonterminal, was not found in name map.) (Residue 304: ALA, Nonterminal, was not found in name map.) (Residue 305: VAL, Nonterminal, was not found in name map.) (Residue 306: GLN, Nonterminal, was not found in name map.) (Residue 307: TYR, Nonterminal, was not found in name map.) (Residue 308: TYR, Nonterminal, was not found in name map.) (Residue 309: THR, Nonterminal, was not found in name map.) (Residue 310: THR, Nonterminal, was not found in name map.) (Residue 311: ARG, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: ILE, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: TYR, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: GLU, Nonterminal, was not found in name map.) (Residue 318: ASN, Nonterminal, was not found in name map.) (Residue 319: LYS, Nonterminal, was not found in name map.) (Residue 320: LYS, Nonterminal, was not found in name map.) (Residue 321: GLY, Nonterminal, was not found in name map.) (Residue 322: GLU, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLY, Nonterminal, was not found in name map.) (Residue 325: ILE, Nonterminal, was not found in name map.) (Residue 326: LEU, Nonterminal, was not found in name map.) (Residue 327: GLN, Nonterminal, was not found in name map.) (Residue 328: ASP, Nonterminal, was not found in name map.) (Residue 329: ALA, Nonterminal, was not found in name map.) (Residue 330: GLU, Nonterminal, was not found in name map.) (Residue 331: ILE, Nonterminal, was not found in name map.) (Residue 332: GLU, Nonterminal, was not found in name map.) (Residue 333: PHE, Nonterminal, was not found in name map.) (Residue 334: PHE, Nonterminal, was not found in name map.) (Residue 335: PRO, Nonterminal, was not found in name map.) (Residue 336: ASP, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: SER, Nonterminal, was not found in name map.) (Residue 339: TRP, Nonterminal, was not found in name map.) (Residue 340: LYS, Nonterminal, was not found in name map.) (Residue 341: ASN, Nonterminal, was not found in name map.) (Residue 342: VAL, Nonterminal, was not found in name map.) (Residue 343: ASP, Nonterminal, was not found in name map.) (Residue 344: TRP, Nonterminal, was not found in name map.) (Residue 345: ILE, Nonterminal, was not found in name map.) (Residue 346: TYR, Nonterminal, was not found in name map.) (Residue 347: VAL, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: PRO, Nonterminal, was not found in name map.) (Residue 350: TRP, Nonterminal, was not found in name map.) (Residue 351: GLY, Nonterminal, was not found in name map.) (Residue 352: VAL, Nonterminal, was not found in name map.) (Residue 353: CYS, Nonterminal, was not found in name map.) (Residue 354: LYS, Nonterminal, was not found in name map.) (Residue 355: LEU, Nonterminal, was not found in name map.) (Residue 356: LEU, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: TYR, Nonterminal, was not found in name map.) (Residue 359: ILE, Nonterminal, was not found in name map.) (Residue 360: LYS, Nonterminal, was not found in name map.) (Residue 361: ASP, Nonterminal, was not found in name map.) (Residue 362: THR, Nonterminal, was not found in name map.) (Residue 363: TYR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: ASN, Nonterminal, was not found in name map.) (Residue 366: PRO, Nonterminal, was not found in name map.) (Residue 367: VAL, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: TYR, Nonterminal, was not found in name map.) (Residue 370: ILE, Nonterminal, was not found in name map.) (Residue 371: THR, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ASN, Nonterminal, was not found in name map.) (Residue 374: GLY, Nonterminal, was not found in name map.) (Residue 375: PHE, Nonterminal, was not found in name map.) (Residue 376: PRO, Nonterminal, was not found in name map.) (Residue 377: GLN, Nonterminal, was not found in name map.) (Residue 378: SER, Nonterminal, was not found in name map.) (Residue 379: ASP, Nonterminal, was not found in name map.) (Residue 380: PRO, Nonterminal, was not found in name map.) (Residue 381: ALA, Nonterminal, was not found in name map.) (Residue 382: PRO, Nonterminal, was not found in name map.) (Residue 383: LEU, Nonterminal, was not found in name map.) (Residue 384: ASP, Nonterminal, was not found in name map.) (Residue 385: ASP, Nonterminal, was not found in name map.) (Residue 386: THR, Nonterminal, was not found in name map.) (Residue 387: GLN, Nonterminal, was not found in name map.) (Residue 388: ARG, Nonterminal, was not found in name map.) (Residue 389: TRP, Nonterminal, was not found in name map.) (Residue 390: GLU, Nonterminal, was not found in name map.) (Residue 391: TYR, Nonterminal, was not found in name map.) (Residue 392: PHE, Nonterminal, was not found in name map.) (Residue 393: ARG, Nonterminal, was not found in name map.) (Residue 394: GLN, Nonterminal, was not found in name map.) (Residue 395: THR, Nonterminal, was not found in name map.) (Residue 396: PHE, Nonterminal, was not found in name map.) (Residue 397: GLN, Nonterminal, was not found in name map.) (Residue 398: GLU, Nonterminal, was not found in name map.) (Residue 399: LEU, Nonterminal, was not found in name map.) (Residue 400: PHE, Nonterminal, was not found in name map.) (Residue 401: LYS, Nonterminal, was not found in name map.) (Residue 402: ALA, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: GLN, Nonterminal, was not found in name map.) (Residue 405: LEU, Nonterminal, was not found in name map.) (Residue 406: ASP, Nonterminal, was not found in name map.) (Residue 407: LYS, Nonterminal, was not found in name map.) (Residue 408: VAL, Nonterminal, was not found in name map.) (Residue 409: ASN, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLN, Nonterminal, was not found in name map.) (Residue 412: VAL, Nonterminal, was not found in name map.) (Residue 413: TYR, Nonterminal, was not found in name map.) (Residue 414: CYS, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: TRP, Nonterminal, was not found in name map.) (Residue 417: SER, Nonterminal, was not found in name map.) (Residue 418: LEU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: ASP, Nonterminal, was not found in name map.) (Residue 421: ASN, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: GLU, Nonterminal, was not found in name map.) (Residue 424: TRP, Nonterminal, was not found in name map.) (Residue 425: ASN, Nonterminal, was not found in name map.) (Residue 426: GLN, Nonterminal, was not found in name map.) (Residue 427: GLY, Nonterminal, was not found in name map.) (Residue 428: TYR, Nonterminal, was not found in name map.) (Residue 429: SER, Nonterminal, was not found in name map.) (Residue 430: SER, Nonterminal, was not found in name map.) (Residue 431: ARG, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: GLY, Nonterminal, was not found in name map.) (Residue 434: LEU, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: HIP, Nonterminal, was not found in name map.) (Residue 437: VAL, Nonterminal, was not found in name map.) (Residue 438: ASP, Nonterminal, was not found in name map.) (Residue 439: PHE, Nonterminal, was not found in name map.) (Residue 440: GLU, Nonterminal, was not found in name map.) (Residue 441: ASP, Nonterminal, was not found in name map.) (Residue 442: PRO, Nonterminal, was not found in name map.) (Residue 443: ALA, Nonterminal, was not found in name map.) (Residue 444: ARG, Nonterminal, was not found in name map.) (Residue 445: PRO, Nonterminal, was not found in name map.) (Residue 446: ARG, Nonterminal, was not found in name map.) (Residue 447: VAL, Nonterminal, was not found in name map.) (Residue 448: PRO, Nonterminal, was not found in name map.) (Residue 449: TYR, Nonterminal, was not found in name map.) (Residue 450: THR, Nonterminal, was not found in name map.) (Residue 451: SER, Nonterminal, was not found in name map.) (Residue 452: ALA, Nonterminal, was not found in name map.) (Residue 453: LYS, Nonterminal, was not found in name map.) (Residue 454: GLU, Nonterminal, was not found in name map.) (Residue 455: TYR, Nonterminal, was not found in name map.) (Residue 456: ALA, Nonterminal, was not found in name map.) (Residue 457: LYS, Nonterminal, was not found in name map.) (Residue 458: ILE, Nonterminal, was not found in name map.) (Residue 459: ILE, Nonterminal, was not found in name map.) (Residue 460: ARG, Nonterminal, was not found in name map.) (Residue 461: ASN, Nonterminal, was not found in name map.) (Residue 462: ASN, Nonterminal, was not found in name map.) (Residue 463: GLY, Nonterminal, was not found in name map.) (Residue 464: LEU, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 465 to: CGLU. (Residue 466: 0GB, Terminal/beginning, was not found in name map.) (Residue 467: UNK, Terminal/last, was not found in name map.) Unknown residue: UNK number: 467 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining NMET - ALA Joining ALA - PHE Joining PHE - PRO Joining PRO - ALA Joining ALA - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - TRP Joining TRP - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - THR Joining THR - ALA Joining ALA - ALA Joining ALA - TYR Joining TYR - GLN Joining GLN - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - GLY Joining GLY - TRP Joining TRP - ASP Joining ASP - ALA Joining ALA - ASP Joining ASP - GLY Joining GLY - LYS Joining LYS - GLY Joining GLY - PRO Joining PRO - CYS Joining CYS - VAL Joining VAL - TRP Joining TRP - ASP Joining ASP - THR Joining THR - PHE Joining PHE - THR Joining THR - HIP Joining HIP - GLN Joining GLN - GLY Joining GLY - GLY Joining GLY - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - PHE Joining PHE - LYS Joining LYS - ASN Joining ASN - GLN Joining GLN - THR Joining THR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - ALA Joining ALA - CYS Joining CYS - GLY Joining GLY - SER Joining SER - TYR Joining TYR - THR Joining THR - LEU Joining LEU - TRP Joining TRP - GLU Joining GLU - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - LYS Joining LYS - CYS Joining CYS - ILE Joining ILE - LYS Joining LYS - GLN Joining GLN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - THR Joining THR - HIE Joining HIE - TYR Joining TYR - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LEU Joining LEU - SER Joining SER - TRP Joining TRP - SER Joining SER - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - ASP Joining ASP - GLY Joining GLY - THR Joining THR - THR Joining THR - GLY Joining GLY - PHE Joining PHE - ILE Joining ILE - ASN Joining ASN - GLN Joining GLN - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - TYR Joining TYR - TYR Joining TYR - ASN Joining ASN - LYS Joining LYS - ILE Joining ILE - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - LEU Joining LEU - LEU Joining LEU - LYS Joining LYS - ASN Joining ASN - GLY Joining GLY - VAL Joining VAL - THR Joining THR - PRO Joining PRO - ILE Joining ILE - VAL Joining VAL - THR Joining THR - LEU Joining LEU - TYR Joining TYR - HIP Joining HIP - PHE Joining PHE - ASP Joining ASP - LEU Joining LEU - PRO Joining PRO - GLN Joining GLN - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - GLN Joining GLN - GLY Joining GLY - GLY Joining GLY - TRP Joining TRP - LEU Joining LEU - SER Joining SER - GLU Joining GLU - ALA Joining ALA - ILE Joining ILE - ILE Joining ILE - GLU Joining GLU - SER Joining SER - PHE Joining PHE - ASP Joining ASP - LYS Joining LYS - TYR Joining TYR - ALA Joining ALA - GLN Joining GLN - PHE Joining PHE - CYS Joining CYS - PHE Joining PHE - SER Joining SER - THR Joining THR - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ARG Joining ARG - VAL Joining VAL - LYS Joining LYS - GLN Joining GLN - TRP Joining TRP - ILE Joining ILE - THR Joining THR - ILE Joining ILE - ASN Joining ASN - GLH Joining GLH - ALA Joining ALA - ASN Joining ASN - VAL Joining VAL - LEU Joining LEU - SER Joining SER - VAL Joining VAL - MET Joining MET - SER Joining SER - TYR Joining TYR - ASP Joining ASP - LEU Joining LEU - GLY Joining GLY - MET Joining MET - PHE Joining PHE - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - HIP Joining HIP - PHE Joining PHE - GLY Joining GLY - THR Joining THR - GLY Joining GLY - GLY Joining GLY - TYR Joining TYR - GLN Joining GLN - ALA Joining ALA - ALA Joining ALA - HIP Joining HIP - ASN Joining ASN - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - ALA Joining ALA - HIE Joining HIE - ALA Joining ALA - ARG Joining ARG - SER Joining SER - TRP Joining TRP - HIP Joining HIP - SER Joining SER - TYR Joining TYR - ASP Joining ASP - SER Joining SER - LEU Joining LEU - PHE Joining PHE - ARG Joining ARG - LYS Joining LYS - LYS Joining LYS - GLN Joining GLN - LYS Joining LYS - GLY Joining GLY - MET Joining MET - VAL Joining VAL - SER Joining SER - LEU Joining LEU - SER Joining SER - LEU Joining LEU - PHE Joining PHE - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - LEU Joining LEU - GLU Joining GLU - PRO Joining PRO - ALA Joining ALA - ASP Joining ASP - PRO Joining PRO - ASN Joining ASN - SER Joining SER - VAL Joining VAL - SER Joining SER - ASP Joining ASP - GLN Joining GLN - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - ALA Joining ALA - ILE Joining ILE - THR Joining THR - PHE Joining PHE - HID Joining HID - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - ALA Joining ALA - LYS Joining LYS - PRO Joining PRO - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - TYR Joining TYR - PRO Joining PRO - GLU Joining GLU - VAL Joining VAL - VAL Joining VAL - LYS Joining LYS - SER Joining SER - GLN Joining GLN - ILE Joining ILE - ALA Joining ALA - SER Joining SER - MET Joining MET - SER Joining SER - GLN Joining GLN - LYS Joining LYS - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - PRO Joining PRO - SER Joining SER - SER Joining SER - ARG Joining ARG - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - PHE Joining PHE - THR Joining THR - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - LYS Joining LYS - MET Joining MET - ILE Joining ILE - LYS Joining LYS - GLY Joining GLY - THR Joining THR - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - ALA Joining ALA - VAL Joining VAL - GLN Joining GLN - TYR Joining TYR - TYR Joining TYR - THR Joining THR - THR Joining THR - ARG Joining ARG - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - TYR Joining TYR - GLN Joining GLN - GLU Joining GLU - ASN Joining ASN - LYS Joining LYS - LYS Joining LYS - GLY Joining GLY - GLU Joining GLU - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - ALA Joining ALA - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - PHE Joining PHE - PHE Joining PHE - PRO Joining PRO - ASP Joining ASP - PRO Joining PRO - SER Joining SER - TRP Joining TRP - LYS Joining LYS - ASN Joining ASN - VAL Joining VAL - ASP Joining ASP - TRP Joining TRP - ILE Joining ILE - TYR Joining TYR - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - TRP Joining TRP - GLY Joining GLY - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - ILE Joining ILE - LYS Joining LYS - ASP Joining ASP - THR Joining THR - TYR Joining TYR - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - VAL Joining VAL - ILE Joining ILE - TYR Joining TYR - ILE Joining ILE - THR Joining THR - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - PHE Joining PHE - PRO Joining PRO - GLN Joining GLN - SER Joining SER - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - PRO Joining PRO - LEU Joining LEU - ASP Joining ASP - ASP Joining ASP - THR Joining THR - GLN Joining GLN - ARG Joining ARG - TRP Joining TRP - GLU Joining GLU - TYR Joining TYR - PHE Joining PHE - ARG Joining ARG - GLN Joining GLN - THR Joining THR - PHE Joining PHE - GLN Joining GLN - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - ALA Joining ALA - ILE Joining ILE - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - VAL Joining VAL - ASN Joining ASN - LEU Joining LEU - GLN Joining GLN - VAL Joining VAL - TYR Joining TYR - CYS Joining CYS - ALA Joining ALA - TRP Joining TRP - SER Joining SER - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - PHE Joining PHE - GLU Joining GLU - TRP Joining TRP - ASN Joining ASN - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - SER Joining SER - SER Joining SER - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - HIP Joining HIP - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLU Joining GLU - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - ARG Joining ARG - PRO Joining PRO - ARG Joining ARG - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - THR Joining THR - SER Joining SER - ALA Joining ALA - LYS Joining LYS - GLU Joining GLU - TYR Joining TYR - ALA Joining ALA - LYS Joining LYS - ILE Joining ILE - ILE Joining ILE - ARG Joining ARG - ASN Joining ASN - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - CGLU Created a new atom named: O1 within residue: .R<0GB 467> Created a new atom named: H7 within residue: .R<0GB 467> Created a new atom named: H8 within residue: .R<0GB 467> Created a new atom named: H9 within residue: .R<0GB 467> Created a new atom named: H10 within residue: .R<0GB 467> Created a new atom named: H11 within residue: .R<0GB 467> Created a new atom named: C14 within residue: .R<0GB 467> Created a new atom named: H15 within residue: .R<0GB 467> Created a new atom named: H16 within residue: .R<0GB 467> Created a new atom named: O17 within residue: .R<0GB 467> Created a new atom named: H18 within residue: .R<0GB 467> Created a new atom named: O19 within residue: .R<0GB 467> Created a new atom named: H20 within residue: .R<0GB 467> Created a new atom named: O21 within residue: .R<0GB 467> Created a new atom named: H22 within residue: .R<0GB 467> Created a new atom named: O23 within residue: .R<0GB 467> Created a new atom named: H24 within residue: .R<0GB 467> Added missing heavy atom: .R<0GB 467>.A Added missing heavy atom: .R<0GB 467>.A Added missing heavy atom: .R<0GB 467>.A Added missing heavy atom: .R<0GB 467>.A Added missing heavy atom: .R<0GB 467>.A Added missing heavy atom: .R<0GB 467>.A Creating new UNIT for residue: UNK sequence: 468 One sided connection. Residue: missing connect0 atom. Created a new atom named: C25 within residue: .R Created a new atom named: N26 within residue: .R Created a new atom named: C27 within residue: .R Created a new atom named: H28 within residue: .R Created a new atom named: H29 within residue: .R Created a new atom named: H30 within residue: .R Created a new atom named: C31 within residue: .R Created a new atom named: H32 within residue: .R Created a new atom named: H33 within residue: .R Created a new atom named: H34 within residue: .R Created a new atom named: O35 within residue: .R Created a new atom named: C36 within residue: .R total atoms in file: 7450 Leap added 17 missing atoms according to residue templates: 6 Heavy 11 H / lone pairs The file contained 29 atoms not in residue templates > bond bglu1.467.C5 bglu1.468.O35 > #check bglu1 > #addions bglu1 Na+ 0 > #saveAmberParm bglu1 gas_bglu1.top gas_bglu1.crd > #savepdb bglu1 bglu1.pdb > #solvateBox bglu1 TIP3PBOX 14.0 > #addIons2 bglu1 Cl- 75.322 > #addIons2 bglu1 Na+ 75.322 > #saveAmberParm bglu1 solvated_bglu1.top solvated_bglu1.crd > #quit > bond bond: Improper number of arguments! usage: bond [order] > bond 7421 7449 bond: Argument #1 is type Double must be of type: [atom] usage: bond [order] > bond 7421 7449 1 bond: Argument #1 is type Double must be of type: [atom] usage: bond [order] > bond C5 O35 bond: Argument #1 is type String must be of type: [atom] usage: bond [order] > bond bglu1.467.C5 bond: Improper number of arguments! usage: bond [order] > bond bglu1.467.C5 bglu1.468.O35 > bond bglu1.467.C5 bglu1.468.O35 1 bond: Argument #3 is type Double must be of type: [string] usage: bond [order] > bond bglu1.467.C5 bglu1.468.O35 virtual bond: Unknown bond order, no bond made. Valid bond orders are: S, D, T, A. > bond bglu1.467.C5 bglu1.468.O35 A > check bglu1 Checking 'bglu1'.... WARNING: There is a bond of 4.687070 angstroms between: ------- .R<0GB 467>.A and .R<0GB 467>.A ERROR: The unperturbed charge of the unit: -4.806000 is not integral. WARNING: The unperturbed charge of the unit: -4.806000 is not zero. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R<0GB 467>.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Warning: Close contact of 1.493745 angstroms between .R.A and .R.A Warning: Close contact of 1.099814 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.237710 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.321238 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.486727 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.313357 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.562832 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.312894 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.360507 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.437703 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.363769 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.178309 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A

Warning: Close contact of 1.122935 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.268081 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.470891 angstroms between .R<0GB 467>.A and .R<0GB 467>.A

Warning: Close contact of 0.988613 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.093276 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.430998 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.230273 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.422533 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.568430 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.313470 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A

Warning: Close contact of 0.702852 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.183464 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.097307 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.414019 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.397593 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.070742 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.049567 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.092771 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.433101 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.335426 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.154238 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.352243 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.926529 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.748290 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.497112 angstroms between .R<0GB 467>.A and .R<0GB 467>.A

Warning: Close contact of 1.073479 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.489993 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.279751 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.460488 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.093846 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.587853 angstroms between .R<0GB 467>.A
and .R<0GB 467>.A Warning: Close contact of 1.313200 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.076136 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.820773 angstroms between .R<0GB 467>.A and .R.A Warning: Close contact of 0.688704 angstroms between .R<0GB 467>.A

and .R<0GB 467>.A Warning: Close contact of 1.387295 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.093326 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.097264 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.415387 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.963659 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.963526 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.965433 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 0.976097 angstroms between .R<0GB 467>.A and .R<0GB 467>.A Warning: Close contact of 1.154974 angstroms between .R.A and .R.A Warning: Close contact of 1.495605 angstroms between .R.A and .R.A Warning: Close contact of 1.091069 angstroms between .R.A and .R.A Warning: Close contact of 1.093944 angstroms between .R.A and .R.A Warning: Close contact of 1.091481 angstroms between .R.A and .R.A Warning: Close contact of 1.093586 angstroms between .R.A and .R.A Warning: Close contact of 1.091622 angstroms between .R.A and .R.A Warning: Close contact of 1.091918 angstroms between .R.A and .R.A Warning: Close contact of 1.403195 angstroms between .R.A and .R.A Checking parameters for unit 'bglu1'. Checking for bond parameters. Could not find bond parameter for: Cg - Could not find bond parameter for: Cg - Could not find bond parameter for: Cg - Checking for angle parameters. Could not find angle parameter: Cg - Cg - Could not find angle parameter: Cg - Cg - Could not find angle parameter: Cg - Cg - Could not find angle parameter: Cg - Cg - Could not find angle parameter: Cg - Cg - Could not find angle parameter: Cg - Cg - Could not find angle parameter: H1 - Cg - Could not find angle parameter: H1 - Cg - Could not find angle parameter: H1 - Cg - Could not find angle parameter: Os - Cg - Could not find angle parameter: Os - Cg - Could not find angle parameter: Os - Cg - There are missing parameters. check: Errors: 30 Warnings: 66 > quit Quit