log started: Thu May 10 14:27:36 2007 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # 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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//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 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static//dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF 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 > source buildit ----- Source: ./buildit ----- Source of ./buildit done >> >> CM5 = loadmol2 cm5.mol2 Loading Mol2 file: ./cm5.mol2 Reading MOLECULE named CM5 >> TMI = loadmol2 tmi.mol2 Could not open file tmi.mol2: not found >> CPZ = loadmol2 cpz.mol2 Loading Mol2 file: ./cpz.mol2 Reading MOLECULE named CPZ >> >> loadoff heme.off Loading library: ./heme.off Loading: HEM >> gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (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) >> heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) >> ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) >> loadoff CYP.off Loading library: ./CYP.off Loading: CYP >> >> >> aa = loadpdb 2BDM_cpz.pdb Loading PDB file: ./2BDM_cpz.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY. (Residue 1: LYS, Nonterminal, was not found in name map.) (Residue 2: LEU, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: PRO, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: PRO, Nonterminal, was not found in name map.) (Residue 7: SER, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: PRO, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASN, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: GLN, Nonterminal, was not found in name map.) (Residue 18: MET, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: LYS, Nonterminal, was not found in name map.) (Residue 22: GLY, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: ARG, Nonterminal, was not found in name map.) (Residue 26: SER, Nonterminal, was not found in name map.) (Residue 27: PHE, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: LEU, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: LYS, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: ASP, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: PHE, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: VAL, Nonterminal, was not found in name map.) (Residue 41: TYR, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: ARG, Nonterminal, was not found in name map.) (Residue 46: PRO, Nonterminal, was not found in name map.) (Residue 47: VAL, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: VAL, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: CYS, Nonterminal, was not found in name map.) (Residue 52: GLY, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: ASP, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: ARG, Nonterminal, was not found in name map.) (Residue 58: GLU, Nonterminal, was not found in name map.) (Residue 59: ALA, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: ASP, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: ALA, Nonterminal, was not found in name map.) (Residue 65: GLU, Nonterminal, was not found in name map.) (Residue 66: ALA, Nonterminal, was not found in name map.) (Residue 67: PHE, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: ARG, Nonterminal, was not found in name map.) (Residue 71: GLY, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: ILE, Nonterminal, was not found in name map.) (Residue 74: ALA, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: VAL, Nonterminal, was not found in name map.) (Residue 77: ASP, Nonterminal, was not found in name map.) (Residue 78: PRO, Nonterminal, was not found in name map.) (Residue 79: ILE, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLN, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: TYR, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: PHE, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: GLY, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: ARG, Nonterminal, was not found in name map.) (Residue 93: TRP, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: ALA, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: SER, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ALA, Nonterminal, was not found in name map.) (Residue 103: THR, Nonterminal, was not found in name map.) (Residue 104: MET, Nonterminal, was not found in name map.) (Residue 105: ARG, Nonterminal, was not found in name map.) (Residue 106: ASP, Nonterminal, was not found in name map.) (Residue 107: PHE, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: MET, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: ARG, Nonterminal, was not found in name map.) (Residue 113: SER, Nonterminal, was not found in name map.) (Residue 114: VAL, Nonterminal, was not found in name map.) (Residue 115: GLU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: ARG, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: GLN, Nonterminal, was not found in name map.) (Residue 120: GLU, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: ARG, Nonterminal, was not found in name map.) (Residue 124: CYS, Nonterminal, was not found in name map.) (Residue 125: LEU, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: GLU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: LYS, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: LYS, Nonterminal, was not found in name map.) (Residue 134: GLY, Nonterminal, was not found in name map.) (Residue 135: ALA, Nonterminal, was not found in name map.) (Residue 136: LEU, Nonterminal, was not found in name map.) (Residue 137: LEU, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: ASN, Nonterminal, was not found in name map.) (Residue 140: THR, Nonterminal, was not found in name map.) (Residue 141: LEU, Nonterminal, was not found in name map.) (Residue 142: LEU, Nonterminal, was not found in name map.) (Residue 143: PHE, Nonterminal, was not found in name map.) (Residue 144: HIE, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: ILE, Nonterminal, was not found in name map.) (Residue 147: THR, Nonterminal, was not found in name map.) (Residue 148: SER, Nonterminal, was not found in name map.) (Residue 149: ASN, Nonterminal, was not found in name map.) (Residue 150: ILE, Nonterminal, was not found in name map.) (Residue 151: ILE, Nonterminal, was not found in name map.) (Residue 152: CYS, Nonterminal, was not found in name map.) (Residue 153: SER, Nonterminal, was not found in name map.) (Residue 154: ILE, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: PHE, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: PHE, Nonterminal, was not found in name map.) (Residue 161: ASP, Nonterminal, was not found in name map.) (Residue 162: TYR, Nonterminal, was not found in name map.) (Residue 163: LYS, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: PRO, Nonterminal, was not found in name map.) (Residue 166: VAL, Nonterminal, was not found in name map.) (Residue 167: PHE, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ARG, Nonterminal, was not found in name map.) (Residue 170: LEU, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: ASP, Nonterminal, was not found in name map.) (Residue 173: LEU, Nonterminal, was not found in name map.) (Residue 174: PHE, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: PHE, Nonterminal, was not found in name map.) (Residue 179: SER, Nonterminal, was not found in name map.) (Residue 180: LEU, Nonterminal, was not found in name map.) (Residue 181: ILE, Nonterminal, was not found in name map.) (Residue 182: SER, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: PHE, Nonterminal, was not found in name map.) (Residue 185: SER, Nonterminal, was not found in name map.) (Residue 186: SER, Nonterminal, was not found in name map.) (Residue 187: GLN, Nonterminal, was not found in name map.) (Residue 188: VAL, Nonterminal, was not found in name map.) (Residue 189: PHE, Nonterminal, was not found in name map.) (Residue 190: GLU, Nonterminal, was not found in name map.) (Residue 191: LEU, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: SER, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: PHE, Nonterminal, was not found in name map.) (Residue 196: LEU, Nonterminal, was not found in name map.) (Residue 197: LYS, Nonterminal, was not found in name map.) (Residue 198: TYR, Nonterminal, was not found in name map.) (Residue 199: PHE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: GLY, Nonterminal, was not found in name map.) (Residue 202: THR, Nonterminal, was not found in name map.) (Residue 203: HID, Nonterminal, was not found in name map.) (Residue 204: ARG, Nonterminal, was not found in name map.) (Residue 205: GLN, Nonterminal, was not found in name map.) (Residue 206: ILE, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: LEU, Nonterminal, was not found in name map.) (Residue 211: GLN, Nonterminal, was not found in name map.) (Residue 212: GLU, Nonterminal, was not found in name map.) (Residue 213: ILE, Nonterminal, was not found in name map.) (Residue 214: ASN, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: PHE, Nonterminal, was not found in name map.) (Residue 217: ILE, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: GLN, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: VAL, Nonterminal, was not found in name map.) (Residue 222: GLU, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: HIE, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: LEU, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ASN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: ARG, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: PHE, Nonterminal, was not found in name map.) (Residue 237: ILE, Nonterminal, was not found in name map.) (Residue 238: ASP, Nonterminal, was not found in name map.) (Residue 239: VAL, Nonterminal, was not found in name map.) (Residue 240: TYR, Nonterminal, was not found in name map.) (Residue 241: LEU, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ARG, Nonterminal, was not found in name map.) (Residue 244: MET, Nonterminal, was not found in name map.) (Residue 245: GLU, Nonterminal, was not found in name map.) (Residue 246: LYS, Nonterminal, was not found in name map.) (Residue 247: ASP, Nonterminal, was not found in name map.) (Residue 248: LYS, Nonterminal, was not found in name map.) (Residue 249: SER, Nonterminal, was not found in name map.) (Residue 250: ASP, Nonterminal, was not found in name map.) (Residue 251: PRO, Nonterminal, was not found in name map.) (Residue 252: SER, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: GLU, Nonterminal, was not found in name map.) (Residue 255: PHE, Nonterminal, was not found in name map.) (Residue 256: HID, Nonterminal, was not found in name map.) (Residue 257: HID, Nonterminal, was not found in name map.) (Residue 258: GLN, Nonterminal, was not found in name map.) (Residue 259: ASN, Nonterminal, was not found in name map.) (Residue 260: LEU, Nonterminal, was not found in name map.) (Residue 261: ILE, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: THR, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: SER, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: PHE, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: ALA, Nonterminal, was not found in name map.) (Residue 271: GLY, Nonterminal, was not found in name map.) (Residue 272: THR, Nonterminal, was not found in name map.) (Residue 273: GLU, Nonterminal, was not found in name map.) (Residue 274: THR, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: SER, Nonterminal, was not found in name map.) (Residue 277: THR, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: LEU, Nonterminal, was not found in name map.) (Residue 280: ARG, Nonterminal, was not found in name map.) (Residue 281: TYR, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: PHE, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: MET, Nonterminal, was not found in name map.) (Residue 287: LEU, Nonterminal, was not found in name map.) (Residue 288: LYS, Nonterminal, was not found in name map.) (Residue 289: TYR, Nonterminal, was not found in name map.) (Residue 290: PRO, Nonterminal, was not found in name map.) (Residue 291: HIE, Nonterminal, was not found in name map.) (Residue 292: VAL, Nonterminal, was not found in name map.) (Residue 293: THR, Nonterminal, was not found in name map.) (Residue 294: GLU, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: VAL, Nonterminal, was not found in name map.) (Residue 297: GLN, Nonterminal, was not found in name map.) (Residue 298: LYS, Nonterminal, was not found in name map.) (Residue 299: GLU, Nonterminal, was not found in name map.) (Residue 300: ILE, Nonterminal, was not found in name map.) (Residue 301: GLU, Nonterminal, was not found in name map.) (Residue 302: GLN, Nonterminal, was not found in name map.) (Residue 303: VAL, Nonterminal, was not found in name map.) (Residue 304: ILE, Nonterminal, was not found in name map.) (Residue 305: GLY, Nonterminal, was not found in name map.) (Residue 306: SER, Nonterminal, was not found in name map.) (Residue 307: HIE, Nonterminal, was not found in name map.) (Residue 308: ARG, Nonterminal, was not found in name map.) (Residue 309: PRO, Nonterminal, was not found in name map.) (Residue 310: PRO, Nonterminal, was not found in name map.) (Residue 311: ALA, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: ASP, Nonterminal, was not found in name map.) (Residue 314: ASP, Nonterminal, was not found in name map.) (Residue 315: ARG, Nonterminal, was not found in name map.) (Residue 316: ALA, Nonterminal, was not found in name map.) (Residue 317: LYS, Nonterminal, was not found in name map.) (Residue 318: MET, Nonterminal, was not found in name map.) (Residue 319: PRO, Nonterminal, was not found in name map.) (Residue 320: TYR, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: ASP, Nonterminal, was not found in name map.) (Residue 323: ALA, Nonterminal, was not found in name map.) (Residue 324: VAL, Nonterminal, was not found in name map.) (Residue 325: ILE, Nonterminal, was not found in name map.) (Residue 326: HIE, Nonterminal, was not found in name map.) (Residue 327: GLU, Nonterminal, was not found in name map.) (Residue 328: ILE, Nonterminal, was not found in name map.) (Residue 329: GLN, Nonterminal, was not found in name map.) (Residue 330: ARG, Nonterminal, was not found in name map.) (Residue 331: LEU, Nonterminal, was not found in name map.) (Residue 332: GLY, Nonterminal, was not found in name map.) (Residue 333: ASP, Nonterminal, was not found in name map.) (Residue 334: LEU, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: PRO, Nonterminal, was not found in name map.) (Residue 337: PHE, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: VAL, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: HID, Nonterminal, was not found in name map.) (Residue 342: THR, Nonterminal, was not found in name map.) (Residue 343: VAL, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: LYS, Nonterminal, was not found in name map.) (Residue 346: ASP, Nonterminal, was not found in name map.) (Residue 347: THR, Nonterminal, was not found in name map.) (Residue 348: GLN, Nonterminal, was not found in name map.) (Residue 349: PHE, Nonterminal, was not found in name map.) (Residue 350: ARG, Nonterminal, was not found in name map.) (Residue 351: GLY, Nonterminal, was not found in name map.) (Residue 352: TYR, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: ILE, Nonterminal, was not found in name map.) (Residue 355: PRO, Nonterminal, was not found in name map.) (Residue 356: LYS, Nonterminal, was not found in name map.) (Residue 357: ASN, Nonterminal, was not found in name map.) (Residue 358: THR, Nonterminal, was not found in name map.) (Residue 359: GLU, Nonterminal, was not found in name map.) (Residue 360: VAL, Nonterminal, was not found in name map.) (Residue 361: PHE, Nonterminal, was not found in name map.) (Residue 362: PRO, Nonterminal, was not found in name map.) (Residue 363: VAL, Nonterminal, was not found in name map.) (Residue 364: LEU, Nonterminal, was not found in name map.) (Residue 365: SER, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: ALA, Nonterminal, was not found in name map.) (Residue 368: LEU, Nonterminal, was not found in name map.) (Residue 369: HID, Nonterminal, was not found in name map.) (Residue 370: ASP, Nonterminal, was not found in name map.) (Residue 371: PRO, Nonterminal, was not found in name map.) (Residue 372: ARG, Nonterminal, was not found in name map.) (Residue 373: TYR, Nonterminal, was not found in name map.) (Residue 374: PHE, Nonterminal, was not found in name map.) (Residue 375: GLU, Nonterminal, was not found in name map.) (Residue 376: THR, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: ASN, Nonterminal, was not found in name map.) (Residue 379: THR, Nonterminal, was not found in name map.) (Residue 380: PHE, Nonterminal, was not found in name map.) (Residue 381: ASN, Nonterminal, was not found in name map.) (Residue 382: PRO, Nonterminal, was not found in name map.) (Residue 383: GLY, Nonterminal, was not found in name map.) (Residue 384: HID, Nonterminal, was not found in name map.) (Residue 385: PHE, Nonterminal, was not found in name map.) (Residue 386: LEU, Nonterminal, was not found in name map.) (Residue 387: ASP, Nonterminal, was not found in name map.) (Residue 388: ALA, Nonterminal, was not found in name map.) (Residue 389: ASN, Nonterminal, was not found in name map.) (Residue 390: GLY, Nonterminal, was not found in name map.) (Residue 391: ALA, Nonterminal, was not found in name map.) (Residue 392: LEU, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: ARG, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: GLU, Nonterminal, was not found in name map.) (Residue 397: GLY, Nonterminal, was not found in name map.) (Residue 398: PHE, Nonterminal, was not found in name map.) (Residue 399: MET, Nonterminal, was not found in name map.) (Residue 400: PRO, Nonterminal, was not found in name map.) (Residue 401: PHE, Nonterminal, was not found in name map.) (Residue 402: SER, Nonterminal, was not found in name map.) (Residue 403: LEU, Nonterminal, was not found in name map.) (Residue 404: GLY, Nonterminal, was not found in name map.) (Residue 405: LYS, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ILE, Nonterminal, was not found in name map.) (Residue 408: CYP, Nonterminal, was not found in name map.) (Residue 409: LEU, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: GLU, Nonterminal, was not found in name map.) (Residue 412: GLY, Nonterminal, was not found in name map.) (Residue 413: ILE, Nonterminal, was not found in name map.) (Residue 414: ALA, Nonterminal, was not found in name map.) (Residue 415: ARG, Nonterminal, was not found in name map.) (Residue 416: THR, Nonterminal, was not found in name map.) (Residue 417: GLU, Nonterminal, was not found in name map.) (Residue 418: LEU, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: LEU, Nonterminal, was not found in name map.) (Residue 421: PHE, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: THR, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: ILE, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: GLN, Nonterminal, was not found in name map.) (Residue 428: ASN, Nonterminal, was not found in name map.) (Residue 429: PHE, Nonterminal, was not found in name map.) (Residue 430: SER, Nonterminal, was not found in name map.) (Residue 431: ILE, Nonterminal, was not found in name map.) (Residue 432: ALA, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: PRO, Nonterminal, was not found in name map.) (Residue 435: VAL, Nonterminal, was not found in name map.) (Residue 436: PRO, Nonterminal, was not found in name map.) (Residue 437: PRO, Nonterminal, was not found in name map.) (Residue 438: GLU, Nonterminal, was not found in name map.) (Residue 439: ASP, Nonterminal, was not found in name map.) (Residue 440: ILE, Nonterminal, was not found in name map.) (Residue 441: ASP, Nonterminal, was not found in name map.) (Residue 442: LEU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: PRO, Nonterminal, was not found in name map.) (Residue 445: ARG, Nonterminal, was not found in name map.) (Residue 446: GLU, Nonterminal, was not found in name map.) (Residue 447: SER, Nonterminal, was not found in name map.) (Residue 448: GLY, Nonterminal, was not found in name map.) (Residue 449: VAL, Nonterminal, was not found in name map.) (Residue 450: GLY, Nonterminal, was not found in name map.) (Residue 451: ASN, Nonterminal, was not found in name map.) (Residue 452: VAL, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: PRO, Nonterminal, was not found in name map.) (Residue 455: SER, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLN, Nonterminal, was not found in name map.) (Residue 458: ILE, Nonterminal, was not found in name map.) (Residue 459: ARG, Nonterminal, was not found in name map.) (Residue 460: PHE, Nonterminal, was not found in name map.) (Residue 461: LEU, Nonterminal, was not found in name map.) (Residue 462: ALA, Nonterminal, was not found in name map.) (Residue 463: ARG, Nonterminal, was not found in name map.) Mapped residue HIE, term: Terminal/last, seq. number: 464 to: CHIE. (Residue 465: HEM, Terminal/last, was not found in name map.) (Residue 466: CPZ, Terminal/last, was not found in name map.) Joining NGLY - LYS Joining LYS - LEU Joining LEU - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - SER Joining SER - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - MET Joining MET - ASP Joining ASP - ARG Joining ARG - LYS Joining LYS - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - SER Joining SER - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - THR Joining THR - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - SER Joining SER - ARG Joining ARG - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - CYS Joining CYS - GLY Joining GLY - THR Joining THR - ASP Joining ASP - ALA Joining ALA - ILE Joining ILE - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - LYS Joining LYS - ILE Joining ILE - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - PRO Joining PRO - ILE Joining ILE - PHE Joining PHE - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - GLU Joining GLU - ARG Joining ARG - TRP Joining TRP - ARG Joining ARG - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LEU Joining LEU - ALA Joining ALA - THR Joining THR - MET Joining MET - ARG Joining ARG - ASP Joining ASP - PHE Joining PHE - GLY Joining GLY - MET Joining MET - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - SER Joining SER - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ARG Joining ARG - CYS Joining CYS - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - LYS Joining LYS - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - THR Joining THR - LEU Joining LEU - LEU Joining LEU - PHE Joining PHE - HIE Joining HIE - SER Joining SER - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ILE Joining ILE - CYS Joining CYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - TYR Joining TYR - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - GLN Joining GLN - SER Joining SER - PHE Joining PHE - SER Joining SER - LEU Joining LEU - ILE Joining ILE - SER Joining SER - SER Joining SER - PHE Joining PHE - SER Joining SER - SER Joining SER - GLN Joining GLN - VAL Joining VAL - PHE Joining PHE - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PHE Joining PHE - PRO Joining PRO - GLY Joining GLY - THR Joining THR - HID Joining HID - ARG Joining ARG - GLN Joining GLN - ILE Joining ILE - TYR Joining TYR - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - THR Joining THR - PHE Joining PHE - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - SER Joining SER - VAL Joining VAL - GLU Joining GLU - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - ALA Joining ALA - THR Joining THR - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - SER Joining SER - ASN Joining ASN - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ASP Joining ASP - LYS Joining LYS - SER Joining SER - ASP Joining ASP - PRO Joining PRO - SER Joining SER - SER Joining SER - GLU Joining GLU - PHE Joining PHE - HID Joining HID - HID Joining HID - GLN Joining GLN - ASN Joining ASN - LEU Joining LEU - ILE Joining ILE - LEU Joining LEU - THR Joining THR - VAL Joining VAL - LEU Joining LEU - SER Joining SER - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - LEU Joining LEU - MET Joining MET - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PRO Joining PRO - HIE Joining HIE - VAL Joining VAL - THR Joining THR - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - LYS Joining LYS - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - SER Joining SER - HIE Joining HIE - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ASP Joining ASP - ASP Joining ASP - ARG Joining ARG - ALA Joining ALA - LYS Joining LYS - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - ILE Joining ILE - GLN Joining GLN - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - ASP Joining ASP - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - PRO Joining PRO - HID Joining HID - THR Joining THR - VAL Joining VAL - THR Joining THR - LYS Joining LYS - ASP Joining ASP - THR Joining THR - GLN Joining GLN - PHE Joining PHE - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - VAL Joining VAL - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - ASN Joining ASN - THR Joining THR - GLU Joining GLU - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - SER Joining SER - SER Joining SER - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - TYR Joining TYR - PHE Joining PHE - GLU Joining GLU - THR Joining THR - PRO Joining PRO - ASN Joining ASN - THR Joining THR - PHE Joining PHE - ASN Joining ASN - PRO Joining PRO - GLY Joining GLY - HID Joining HID - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - LYS Joining LYS - ARG Joining ARG - ASN Joining ASN - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - MET Joining MET - PRO Joining PRO - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - ILE Joining ILE - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - ILE Joining ILE - ALA Joining ALA - ARG Joining ARG - THR Joining THR - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - THR Joining THR - ILE Joining ILE - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - SER Joining SER - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - ASP Joining ASP - ILE Joining ILE - ASP Joining ASP - LEU Joining LEU - THR Joining THR - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - SER Joining SER - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - ASN Joining ASN - VAL Joining VAL - PRO Joining PRO - PRO Joining PRO - SER Joining SER - TYR Joining TYR - GLN Joining GLN - ILE Joining ILE - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - CHIE total atoms in file: 7573 >> bond aa.409.SG aa.466.FE >> >> saveamberparm aa 2BDM_cpz_vac.topo 2BDM_cpz_vac.coords Checking Unit. WARNING: The unperturbed charge of the unit: 3.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1578 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CHIE 1 CPZ 1 HEM 1 NGLY 1 ) (no restraints) >> >> #solvateoct aa TIP3PBOX 12.0 iso >> >> #addions aa Cl- 0 >> >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> #addions aa Na+ 10 Cl- 10 >> >> #saveamberparm aa 1SUO.topo 1SUO.coords > > quit Quit log started: Thu May 10 16:14:55 2007 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # 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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/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 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/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: /uufs/inscc.utah.edu/common/home/cheatham/dirs/amberfs/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF 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 > source buildit ----- Source: ./buildit ----- Source of ./buildit done >> >> CM5 = loadmol2 cm5.mol2 Loading Mol2 file: ./cm5.mol2 Reading MOLECULE named CM5 >> TMI = loadmol2 tmi.mol2 Could not open file tmi.mol2: not found >> CPZ = loadmol2 cpz.mol2 Loading Mol2 file: ./cpz.mol2 Reading MOLECULE named CPZ >> >> loadoff heme.off Loading library: ./heme.off Loading: HEM >> gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (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) >> heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) >> ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) >> loadoff CYP.off Loading library: ./CYP.off Loading: CYP >> >> >> #aa = loadpdb 2BDM_cpz.pdb >> aa = loadpdb min.pdb Loading PDB file: ./min.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY. (Residue 1: LYS, Nonterminal, was not found in name map.) (Residue 2: LEU, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: PRO, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: PRO, Nonterminal, was not found in name map.) (Residue 7: SER, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: PRO, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASN, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: GLN, Nonterminal, was not found in name map.) (Residue 18: MET, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: LYS, Nonterminal, was not found in name map.) (Residue 22: GLY, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: ARG, Nonterminal, was not found in name map.) (Residue 26: SER, Nonterminal, was not found in name map.) (Residue 27: PHE, Nonterminal, was not found in name map.) (Residue 28: LEU, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: LEU, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: LYS, Nonterminal, was not found in name map.) (Residue 34: TYR, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: ASP, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: PHE, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: VAL, Nonterminal, was not found in name map.) (Residue 41: TYR, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: SER, Nonterminal, was not found in name map.) (Residue 45: ARG, Nonterminal, was not found in name map.) (Residue 46: PRO, Nonterminal, was not found in name map.) (Residue 47: VAL, Nonterminal, was not found in name map.) (Residue 48: VAL, Nonterminal, was not found in name map.) (Residue 49: VAL, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: CYS, Nonterminal, was not found in name map.) (Residue 52: GLY, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: ASP, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: ARG, Nonterminal, was not found in name map.) (Residue 58: GLU, Nonterminal, was not found in name map.) (Residue 59: ALA, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: ASP, Nonterminal, was not found in name map.) (Residue 63: GLN, Nonterminal, was not found in name map.) (Residue 64: ALA, Nonterminal, was not found in name map.) (Residue 65: GLU, Nonterminal, was not found in name map.) (Residue 66: ALA, Nonterminal, was not found in name map.) (Residue 67: PHE, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: ARG, Nonterminal, was not found in name map.) (Residue 71: GLY, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: ILE, Nonterminal, was not found in name map.) (Residue 74: ALA, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: VAL, Nonterminal, was not found in name map.) (Residue 77: ASP, Nonterminal, was not found in name map.) (Residue 78: PRO, Nonterminal, was not found in name map.) (Residue 79: ILE, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLN, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: TYR, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: ILE, Nonterminal, was not found in name map.) (Residue 87: PHE, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: GLY, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: ARG, Nonterminal, was not found in name map.) (Residue 93: TRP, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: ALA, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: SER, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ALA, Nonterminal, was not found in name map.) (Residue 103: THR, Nonterminal, was not found in name map.) (Residue 104: MET, Nonterminal, was not found in name map.) (Residue 105: ARG, Nonterminal, was not found in name map.) (Residue 106: ASP, Nonterminal, was not found in name map.) (Residue 107: PHE, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: MET, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: ARG, Nonterminal, was not found in name map.) (Residue 113: SER, Nonterminal, was not found in name map.) (Residue 114: VAL, Nonterminal, was not found in name map.) (Residue 115: GLU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: ARG, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: GLN, Nonterminal, was not found in name map.) (Residue 120: GLU, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: ARG, Nonterminal, was not found in name map.) (Residue 124: CYS, Nonterminal, was not found in name map.) (Residue 125: LEU, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: GLU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: LYS, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: LYS, Nonterminal, was not found in name map.) (Residue 134: GLY, Nonterminal, was not found in name map.) (Residue 135: ALA, Nonterminal, was not found in name map.) (Residue 136: LEU, Nonterminal, was not found in name map.) (Residue 137: LEU, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: ASN, Nonterminal, was not found in name map.) (Residue 140: THR, Nonterminal, was not found in name map.) (Residue 141: LEU, Nonterminal, was not found in name map.) (Residue 142: LEU, Nonterminal, was not found in name map.) (Residue 143: PHE, Nonterminal, was not found in name map.) (Residue 144: HIE, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: ILE, Nonterminal, was not found in name map.) (Residue 147: THR, Nonterminal, was not found in name map.) (Residue 148: SER, Nonterminal, was not found in name map.) (Residue 149: ASN, Nonterminal, was not found in name map.) (Residue 150: ILE, Nonterminal, was not found in name map.) (Residue 151: ILE, Nonterminal, was not found in name map.) (Residue 152: CYS, Nonterminal, was not found in name map.) (Residue 153: SER, Nonterminal, was not found in name map.) (Residue 154: ILE, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: PHE, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: PHE, Nonterminal, was not found in name map.) (Residue 161: ASP, Nonterminal, was not found in name map.) (Residue 162: TYR, Nonterminal, was not found in name map.) (Residue 163: LYS, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: PRO, Nonterminal, was not found in name map.) (Residue 166: VAL, Nonterminal, was not found in name map.) (Residue 167: PHE, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ARG, Nonterminal, was not found in name map.) (Residue 170: LEU, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: ASP, Nonterminal, was not found in name map.) (Residue 173: LEU, Nonterminal, was not found in name map.) (Residue 174: PHE, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: SER, Nonterminal, was not found in name map.) (Residue 178: PHE, Nonterminal, was not found in name map.) (Residue 179: SER, Nonterminal, was not found in name map.) (Residue 180: LEU, Nonterminal, was not found in name map.) (Residue 181: ILE, Nonterminal, was not found in name map.) (Residue 182: SER, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: PHE, Nonterminal, was not found in name map.) (Residue 185: SER, Nonterminal, was not found in name map.) (Residue 186: SER, Nonterminal, was not found in name map.) (Residue 187: GLN, Nonterminal, was not found in name map.) (Residue 188: VAL, Nonterminal, was not found in name map.) (Residue 189: PHE, Nonterminal, was not found in name map.) (Residue 190: GLU, Nonterminal, was not found in name map.) (Residue 191: LEU, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: SER, Nonterminal, was not found in name map.) (Residue 194: GLY, Nonterminal, was not found in name map.) (Residue 195: PHE, Nonterminal, was not found in name map.) (Residue 196: LEU, Nonterminal, was not found in name map.) (Residue 197: LYS, Nonterminal, was not found in name map.) (Residue 198: TYR, Nonterminal, was not found in name map.) (Residue 199: PHE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: GLY, Nonterminal, was not found in name map.) (Residue 202: THR, Nonterminal, was not found in name map.) (Residue 203: HID, Nonterminal, was not found in name map.) (Residue 204: ARG, Nonterminal, was not found in name map.) (Residue 205: GLN, Nonterminal, was not found in name map.) (Residue 206: ILE, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: LEU, Nonterminal, was not found in name map.) (Residue 211: GLN, Nonterminal, was not found in name map.) (Residue 212: GLU, Nonterminal, was not found in name map.) (Residue 213: ILE, Nonterminal, was not found in name map.) (Residue 214: ASN, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: PHE, Nonterminal, was not found in name map.) (Residue 217: ILE, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: GLN, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: VAL, Nonterminal, was not found in name map.) (Residue 222: GLU, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: HIE, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: LEU, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ASN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: ARG, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: PHE, Nonterminal, was not found in name map.) (Residue 237: ILE, Nonterminal, was not found in name map.) (Residue 238: ASP, Nonterminal, was not found in name map.) (Residue 239: VAL, Nonterminal, was not found in name map.) (Residue 240: TYR, Nonterminal, was not found in name map.) (Residue 241: LEU, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ARG, Nonterminal, was not found in name map.) (Residue 244: MET, Nonterminal, was not found in name map.) (Residue 245: GLU, Nonterminal, was not found in name map.) (Residue 246: LYS, Nonterminal, was not found in name map.) (Residue 247: ASP, Nonterminal, was not found in name map.) (Residue 248: LYS, Nonterminal, was not found in name map.) (Residue 249: SER, Nonterminal, was not found in name map.) (Residue 250: ASP, Nonterminal, was not found in name map.) (Residue 251: PRO, Nonterminal, was not found in name map.) (Residue 252: SER, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: GLU, Nonterminal, was not found in name map.) (Residue 255: PHE, Nonterminal, was not found in name map.) (Residue 256: HID, Nonterminal, was not found in name map.) (Residue 257: HID, Nonterminal, was not found in name map.) (Residue 258: GLN, Nonterminal, was not found in name map.) (Residue 259: ASN, Nonterminal, was not found in name map.) (Residue 260: LEU, Nonterminal, was not found in name map.) (Residue 261: ILE, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: THR, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: SER, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: PHE, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: ALA, Nonterminal, was not found in name map.) (Residue 271: GLY, Nonterminal, was not found in name map.) (Residue 272: THR, Nonterminal, was not found in name map.) (Residue 273: GLU, Nonterminal, was not found in name map.) (Residue 274: THR, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: SER, Nonterminal, was not found in name map.) (Residue 277: THR, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: LEU, Nonterminal, was not found in name map.) (Residue 280: ARG, Nonterminal, was not found in name map.) (Residue 281: TYR, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: PHE, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: MET, Nonterminal, was not found in name map.) (Residue 287: LEU, Nonterminal, was not found in name map.) (Residue 288: LYS, Nonterminal, was not found in name map.) (Residue 289: TYR, Nonterminal, was not found in name map.) (Residue 290: PRO, Nonterminal, was not found in name map.) (Residue 291: HIE, Nonterminal, was not found in name map.) (Residue 292: VAL, Nonterminal, was not found in name map.) (Residue 293: THR, Nonterminal, was not found in name map.) (Residue 294: GLU, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: VAL, Nonterminal, was not found in name map.) (Residue 297: GLN, Nonterminal, was not found in name map.) (Residue 298: LYS, Nonterminal, was not found in name map.) (Residue 299: GLU, Nonterminal, was not found in name map.) (Residue 300: ILE, Nonterminal, was not found in name map.) (Residue 301: GLU, Nonterminal, was not found in name map.) (Residue 302: GLN, Nonterminal, was not found in name map.) (Residue 303: VAL, Nonterminal, was not found in name map.) (Residue 304: ILE, Nonterminal, was not found in name map.) (Residue 305: GLY, Nonterminal, was not found in name map.) (Residue 306: SER, Nonterminal, was not found in name map.) (Residue 307: HIE, Nonterminal, was not found in name map.) (Residue 308: ARG, Nonterminal, was not found in name map.) (Residue 309: PRO, Nonterminal, was not found in name map.) (Residue 310: PRO, Nonterminal, was not found in name map.) (Residue 311: ALA, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: ASP, Nonterminal, was not found in name map.) (Residue 314: ASP, Nonterminal, was not found in name map.) (Residue 315: ARG, Nonterminal, was not found in name map.) (Residue 316: ALA, Nonterminal, was not found in name map.) (Residue 317: LYS, Nonterminal, was not found in name map.) (Residue 318: MET, Nonterminal, was not found in name map.) (Residue 319: PRO, Nonterminal, was not found in name map.) (Residue 320: TYR, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: ASP, Nonterminal, was not found in name map.) (Residue 323: ALA, Nonterminal, was not found in name map.) (Residue 324: VAL, Nonterminal, was not found in name map.) (Residue 325: ILE, Nonterminal, was not found in name map.) (Residue 326: HIE, Nonterminal, was not found in name map.) (Residue 327: GLU, Nonterminal, was not found in name map.) (Residue 328: ILE, Nonterminal, was not found in name map.) (Residue 329: GLN, Nonterminal, was not found in name map.) (Residue 330: ARG, Nonterminal, was not found in name map.) (Residue 331: LEU, Nonterminal, was not found in name map.) (Residue 332: GLY, Nonterminal, was not found in name map.) (Residue 333: ASP, Nonterminal, was not found in name map.) (Residue 334: LEU, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: PRO, Nonterminal, was not found in name map.) (Residue 337: PHE, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: VAL, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: HID, Nonterminal, was not found in name map.) (Residue 342: THR, Nonterminal, was not found in name map.) (Residue 343: VAL, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: LYS, Nonterminal, was not found in name map.) (Residue 346: ASP, Nonterminal, was not found in name map.) (Residue 347: THR, Nonterminal, was not found in name map.) (Residue 348: GLN, Nonterminal, was not found in name map.) (Residue 349: PHE, Nonterminal, was not found in name map.) (Residue 350: ARG, Nonterminal, was not found in name map.) (Residue 351: GLY, Nonterminal, was not found in name map.) (Residue 352: TYR, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: ILE, Nonterminal, was not found in name map.) (Residue 355: PRO, Nonterminal, was not found in name map.) (Residue 356: LYS, Nonterminal, was not found in name map.) (Residue 357: ASN, Nonterminal, was not found in name map.) (Residue 358: THR, Nonterminal, was not found in name map.) (Residue 359: GLU, Nonterminal, was not found in name map.) (Residue 360: VAL, Nonterminal, was not found in name map.) (Residue 361: PHE, Nonterminal, was not found in name map.) (Residue 362: PRO, Nonterminal, was not found in name map.) (Residue 363: VAL, Nonterminal, was not found in name map.) (Residue 364: LEU, Nonterminal, was not found in name map.) (Residue 365: SER, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: ALA, Nonterminal, was not found in name map.) (Residue 368: LEU, Nonterminal, was not found in name map.) (Residue 369: HID, Nonterminal, was not found in name map.) (Residue 370: ASP, Nonterminal, was not found in name map.) (Residue 371: PRO, Nonterminal, was not found in name map.) (Residue 372: ARG, Nonterminal, was not found in name map.) (Residue 373: TYR, Nonterminal, was not found in name map.) (Residue 374: PHE, Nonterminal, was not found in name map.) (Residue 375: GLU, Nonterminal, was not found in name map.) (Residue 376: THR, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: ASN, Nonterminal, was not found in name map.) (Residue 379: THR, Nonterminal, was not found in name map.) (Residue 380: PHE, Nonterminal, was not found in name map.) (Residue 381: ASN, Nonterminal, was not found in name map.) (Residue 382: PRO, Nonterminal, was not found in name map.) (Residue 383: GLY, Nonterminal, was not found in name map.) (Residue 384: HID, Nonterminal, was not found in name map.) (Residue 385: PHE, Nonterminal, was not found in name map.) (Residue 386: LEU, Nonterminal, was not found in name map.) (Residue 387: ASP, Nonterminal, was not found in name map.) (Residue 388: ALA, Nonterminal, was not found in name map.) (Residue 389: ASN, Nonterminal, was not found in name map.) (Residue 390: GLY, Nonterminal, was not found in name map.) (Residue 391: ALA, Nonterminal, was not found in name map.) (Residue 392: LEU, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: ARG, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: GLU, Nonterminal, was not found in name map.) (Residue 397: GLY, Nonterminal, was not found in name map.) (Residue 398: PHE, Nonterminal, was not found in name map.) (Residue 399: MET, Nonterminal, was not found in name map.) (Residue 400: PRO, Nonterminal, was not found in name map.) (Residue 401: PHE, Nonterminal, was not found in name map.) (Residue 402: SER, Nonterminal, was not found in name map.) (Residue 403: LEU, Nonterminal, was not found in name map.) (Residue 404: GLY, Nonterminal, was not found in name map.) (Residue 405: LYS, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ILE, Nonterminal, was not found in name map.) (Residue 408: CYP, Nonterminal, was not found in name map.) (Residue 409: LEU, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: GLU, Nonterminal, was not found in name map.) (Residue 412: GLY, Nonterminal, was not found in name map.) (Residue 413: ILE, Nonterminal, was not found in name map.) (Residue 414: ALA, Nonterminal, was not found in name map.) (Residue 415: ARG, Nonterminal, was not found in name map.) (Residue 416: THR, Nonterminal, was not found in name map.) (Residue 417: GLU, Nonterminal, was not found in name map.) (Residue 418: LEU, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: LEU, Nonterminal, was not found in name map.) (Residue 421: PHE, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: THR, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: ILE, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: GLN, Nonterminal, was not found in name map.) (Residue 428: ASN, Nonterminal, was not found in name map.) (Residue 429: PHE, Nonterminal, was not found in name map.) (Residue 430: SER, Nonterminal, was not found in name map.) (Residue 431: ILE, Nonterminal, was not found in name map.) (Residue 432: ALA, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: PRO, Nonterminal, was not found in name map.) (Residue 435: VAL, Nonterminal, was not found in name map.) (Residue 436: PRO, Nonterminal, was not found in name map.) (Residue 437: PRO, Nonterminal, was not found in name map.) (Residue 438: GLU, Nonterminal, was not found in name map.) (Residue 439: ASP, Nonterminal, was not found in name map.) (Residue 440: ILE, Nonterminal, was not found in name map.) (Residue 441: ASP, Nonterminal, was not found in name map.) (Residue 442: LEU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: PRO, Nonterminal, was not found in name map.) (Residue 445: ARG, Nonterminal, was not found in name map.) (Residue 446: GLU, Nonterminal, was not found in name map.) (Residue 447: SER, Nonterminal, was not found in name map.) (Residue 448: GLY, Nonterminal, was not found in name map.) (Residue 449: VAL, Nonterminal, was not found in name map.) (Residue 450: GLY, Nonterminal, was not found in name map.) (Residue 451: ASN, Nonterminal, was not found in name map.) (Residue 452: VAL, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: PRO, Nonterminal, was not found in name map.) (Residue 455: SER, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLN, Nonterminal, was not found in name map.) (Residue 458: ILE, Nonterminal, was not found in name map.) (Residue 459: ARG, Nonterminal, was not found in name map.) (Residue 460: PHE, Nonterminal, was not found in name map.) (Residue 461: LEU, Nonterminal, was not found in name map.) (Residue 462: ALA, Nonterminal, was not found in name map.) (Residue 463: ARG, Nonterminal, was not found in name map.) Mapped residue HIE, term: Terminal/last, seq. number: 464 to: CHIE. (Residue 465: HEM, Terminal/last, was not found in name map.) (Residue 466: CPZ, Terminal/last, was not found in name map.) Joining NGLY - LYS Joining LYS - LEU Joining LEU - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - SER Joining SER - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - MET Joining MET - ASP Joining ASP - ARG Joining ARG - LYS Joining LYS - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - SER Joining SER - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - THR Joining THR - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - SER Joining SER - ARG Joining ARG - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - CYS Joining CYS - GLY Joining GLY - THR Joining THR - ASP Joining ASP - ALA Joining ALA - ILE Joining ILE - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - LYS Joining LYS - ILE Joining ILE - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - PRO Joining PRO - ILE Joining ILE - PHE Joining PHE - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - GLU Joining GLU - ARG Joining ARG - TRP Joining TRP - ARG Joining ARG - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LEU Joining LEU - ALA Joining ALA - THR Joining THR - MET Joining MET - ARG Joining ARG - ASP Joining ASP - PHE Joining PHE - GLY Joining GLY - MET Joining MET - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - SER Joining SER - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ARG Joining ARG - CYS Joining CYS - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - LYS Joining LYS - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - THR Joining THR - LEU Joining LEU - LEU Joining LEU - PHE Joining PHE - HIE Joining HIE - SER Joining SER - ILE Joining ILE - THR Joining THR - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ILE Joining ILE - CYS Joining CYS - SER Joining SER - ILE Joining ILE - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - TYR Joining TYR - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - GLN Joining GLN - SER Joining SER - PHE Joining PHE - SER Joining SER - LEU Joining LEU - ILE Joining ILE - SER Joining SER - SER Joining SER - PHE Joining PHE - SER Joining SER - SER Joining SER - GLN Joining GLN - VAL Joining VAL - PHE Joining PHE - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PHE Joining PHE - PRO Joining PRO - GLY Joining GLY - THR Joining THR - HID Joining HID - ARG Joining ARG - GLN Joining GLN - ILE Joining ILE - TYR Joining TYR - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - THR Joining THR - PHE Joining PHE - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - SER Joining SER - VAL Joining VAL - GLU Joining GLU - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - ALA Joining ALA - THR Joining THR - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - SER Joining SER - ASN Joining ASN - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ASP Joining ASP - LYS Joining LYS - SER Joining SER - ASP Joining ASP - PRO Joining PRO - SER Joining SER - SER Joining SER - GLU Joining GLU - PHE Joining PHE - HID Joining HID - HID Joining HID - GLN Joining GLN - ASN Joining ASN - LEU Joining LEU - ILE Joining ILE - LEU Joining LEU - THR Joining THR - VAL Joining VAL - LEU Joining LEU - SER Joining SER - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - THR Joining THR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - LEU Joining LEU - MET Joining MET - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PRO Joining PRO - HIE Joining HIE - VAL Joining VAL - THR Joining THR - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - LYS Joining LYS - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - SER Joining SER - HIE Joining HIE - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ASP Joining ASP - ASP Joining ASP - ARG Joining ARG - ALA Joining ALA - LYS Joining LYS - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - ILE Joining ILE - GLN Joining GLN - ARG Joining ARG - LEU Joining LEU - GLY Joining GLY - ASP Joining ASP - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - PRO Joining PRO - HID Joining HID - THR Joining THR - VAL Joining VAL - THR Joining THR - LYS Joining LYS - ASP Joining ASP - THR Joining THR - GLN Joining GLN - PHE Joining PHE - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - VAL Joining VAL - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - ASN Joining ASN - THR Joining THR - GLU Joining GLU - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - SER Joining SER - SER Joining SER - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - TYR Joining TYR - PHE Joining PHE - GLU Joining GLU - THR Joining THR - PRO Joining PRO - ASN Joining ASN - THR Joining THR - PHE Joining PHE - ASN Joining ASN - PRO Joining PRO - GLY Joining GLY - HID Joining HID - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - ALA Joining ALA - LEU Joining LEU - LYS Joining LYS - ARG Joining ARG - ASN Joining ASN - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - MET Joining MET - PRO Joining PRO - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - ARG Joining ARG - ILE Joining ILE - CYP Joining CYP - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - ILE Joining ILE - ALA Joining ALA - ARG Joining ARG - THR Joining THR - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - THR Joining THR - ILE Joining ILE - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - SER Joining SER - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - ASP Joining ASP - ILE Joining ILE - ASP Joining ASP - LEU Joining LEU - THR Joining THR - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - SER Joining SER - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - ASN Joining ASN - VAL Joining VAL - PRO Joining PRO - PRO Joining PRO - SER Joining SER - TYR Joining TYR - GLN Joining GLN - ILE Joining ILE - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - CHIE total atoms in file: 7573 >> >> bond aa.409.SG aa.466.FE >> >> #saveamberparm aa 2BDM_cpz_vac.topo 2BDM_cpz_vac.coords >> >> solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.380659 to meet diagonal cut criterion Solute vdw bounding box: 72.593 51.721 72.333 Total bounding box for atom centers: 105.729 105.729 105.729 (box expansion for 'iso' is 24.9%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 607872.865 A^3 (oct) Total mass 324074.446 amu, Density 0.885 g/cc Added 15012 residues. >> >> addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -42.32 -44.12 -47.45 46.05 39.28 39.94 sized: 85.68 83.88 80.55 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.61% of box, grid points 96770 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 116 sec (Replacing solvent molecule) Placed Cl- in aa at (-6.95, -9.00, -14.05). (Replacing solvent molecule) Placed Cl- in aa at (2.09, 11.82, -41.11). (Replacing solvent molecule) Placed Cl- in aa at (-14.10, -14.01, -11.85). Done adding ions. >> >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -48.90 45.37 38.60 39.26 sized: 86.36 84.56 79.10 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.14% of box, grid points 107765 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 125 sec (Replacing solvent molecule) Placed Na+ in aa at (29.17, 6.73, -6.62). (Replacing solvent molecule) Placed Cl- in aa at (1.59, -4.70, -22.72). (Replacing solvent molecule) Placed Na+ in aa at (4.45, -4.29, -22.11). (Replacing solvent molecule) Placed Cl- in aa at (6.80, -6.64, -21.48). (Replacing solvent molecule) Placed Na+ in aa at (4.34, -6.54, -23.64). (Replacing solvent molecule) Placed Cl- in aa at (8.19, -8.84, -19.31). (Replacing solvent molecule) Placed Na+ in aa at (13.96, -23.34, -1.92). (Replacing solvent molecule) Placed Cl- in aa at (5.45, -2.07, -27.12). (Replacing solvent molecule) Placed Na+ in aa at (10.25, -7.92, -26.21). (Replacing solvent molecule) Placed Cl- in aa at (-15.40, -25.83, 14.29). (Replacing solvent molecule) Placed Na+ in aa at (9.85, -1.73, 34.17). (Replacing solvent molecule) Placed Cl- in aa at (10.61, 0.01, 36.09). (Replacing solvent molecule) Placed Na+ in aa at (10.13, 5.60, 33.37). (Replacing solvent molecule) Placed Cl- in aa at (14.70, -9.30, 29.56). (Replacing solvent molecule) Placed Na+ in aa at (12.51, -2.63, 35.94). (Replacing solvent molecule) Placed Cl- in aa at (-21.04, 21.01, -0.99). (Replacing solvent molecule) Placed Na+ in aa at (-21.55, 14.61, 3.07). (Replacing solvent molecule) Placed Cl- in aa at (-20.73, 14.66, -1.53). (Replacing solvent molecule) Placed Na+ in aa at (-26.79, 19.44, -6.62). (Replacing solvent molecule) Placed Cl- in aa at (-25.45, 17.33, 4.80). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -48.90 45.37 38.60 43.88 sized: 86.36 84.56 79.10 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.28% of box, grid points 110672 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 130 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.37, 20.92, -31.47). (Replacing solvent molecule) Placed Cl- in aa at (-5.14, 15.06, -42.90). (Replacing solvent molecule) Placed Na+ in aa at (-5.33, 14.01, -37.51). (Replacing solvent molecule) Placed Cl- in aa at (-5.80, 17.93, -36.09). (Replacing solvent molecule) Placed Na+ in aa at (-8.09, 13.94, -35.72). (Replacing solvent molecule) Placed Cl- in aa at (-7.15, 11.94, -37.57). (Replacing solvent molecule) Placed Na+ in aa at (-6.16, 12.73, -44.08). (Replacing solvent molecule) Placed Cl- in aa at (6.65, -8.74, -27.30). (Replacing solvent molecule) Placed Na+ in aa at (4.13, -7.30, -30.13). (Replacing solvent molecule) Placed Cl- in aa at (1.90, -5.49, -32.88). (Replacing solvent molecule) Placed Na+ in aa at (1.78, -2.34, -30.20). (Replacing solvent molecule) Placed Cl- in aa at (3.26, 3.88, -27.29). (Replacing solvent molecule) Placed Na+ in aa at (-1.23, 3.70, -27.83). (No solvent overlap) Placed Cl- in aa at (-5.64, 4.56, -26.90). (Replacing solvent molecule) Placed Na+ in aa at (-9.06, 3.85, -28.26). (Replacing solvent molecule) Placed Cl- in aa at (-8.93, 1.86, -32.49). (Replacing solvent molecule) Placed Na+ in aa at (-9.77, -1.57, -29.37). (Replacing solvent molecule) Placed Cl- in aa at (-13.15, 2.59, -29.91). (Replacing solvent molecule) Placed Na+ in aa at (-11.70, 4.78, -32.38). (Replacing solvent molecule) Placed Cl- in aa at (-6.19, -3.66, -31.74). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -51.87 45.37 38.60 43.88 sized: 86.36 84.56 76.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.38% of box, grid points 112864 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 134 sec (Replacing solvent molecule) Placed Na+ in aa at (23.68, -14.99, 20.15). (Replacing solvent molecule) Placed Cl- in aa at (23.46, -17.67, 22.90). (Replacing solvent molecule) Placed Na+ in aa at (19.25, -20.64, 20.46). (Replacing solvent molecule) Placed Cl- in aa at (28.75, -15.91, 17.90). (Replacing solvent molecule) Placed Na+ in aa at (32.93, -12.87, 19.75). (Replacing solvent molecule) Placed Cl- in aa at (32.87, -11.07, 17.16). (Replacing solvent molecule) Placed Na+ in aa at (32.39, -16.40, 17.27). (Replacing solvent molecule) Placed Cl- in aa at (0.30, -6.32, -28.71). (Replacing solvent molecule) Placed Na+ in aa at (-2.43, -5.31, -32.65). (Replacing solvent molecule) Placed Cl- in aa at (-0.77, 1.26, -29.07). (Replacing solvent molecule) Placed Na+ in aa at (-1.54, -1.80, -29.53). (Replacing solvent molecule) Placed Cl- in aa at (35.74, -16.55, 21.56). (Replacing solvent molecule) Placed Na+ in aa at (30.89, -13.98, 17.35). (Replacing solvent molecule) Placed Cl- in aa at (29.60, -12.71, 19.49). (Replacing solvent molecule) Placed Na+ in aa at (28.19, -18.06, 21.17). (Replacing solvent molecule) Placed Cl- in aa at (-12.17, -4.40, -28.43). (Replacing solvent molecule) Placed Na+ in aa at (-16.16, -9.05, -27.27). (Replacing solvent molecule) Placed Cl- in aa at (-14.78, -8.52, -24.97). (Replacing solvent molecule) Placed Na+ in aa at (-14.21, -5.89, -24.76). (Replacing solvent molecule) Placed Cl- in aa at (-18.43, -5.61, -25.68). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -51.87 45.37 38.60 43.88 sized: 86.36 84.56 76.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.50% of box, grid points 115284 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 136 sec (Replacing solvent molecule) Placed Na+ in aa at (5.36, 24.61, -29.37). (Replacing solvent molecule) Placed Cl- in aa at (4.43, 28.12, -33.83). (Replacing solvent molecule) Placed Na+ in aa at (4.45, 25.66, -34.82). (Replacing solvent molecule) Placed Cl- in aa at (-0.80, 23.26, -30.86). (Replacing solvent molecule) Placed Na+ in aa at (-1.83, 21.83, -28.72). (Replacing solvent molecule) Placed Cl- in aa at (11.69, 30.74, -9.53). (Replacing solvent molecule) Placed Na+ in aa at (14.18, 32.38, -12.78). (Replacing solvent molecule) Placed Cl- in aa at (12.62, 35.98, -16.92). (Replacing solvent molecule) Placed Na+ in aa at (7.42, 34.17, -14.40). (Replacing solvent molecule) Placed Cl- in aa at (2.35, 35.88, -13.74). (Replacing solvent molecule) Placed Na+ in aa at (5.53, 31.66, -19.10). (Replacing solvent molecule) Placed Cl- in aa at (4.65, 34.67, -18.46). (Replacing solvent molecule) Placed Na+ in aa at (-1.33, 33.92, -15.15). (Replacing solvent molecule) Placed Cl- in aa at (-3.40, 32.16, -14.21). (Replacing solvent molecule) Placed Na+ in aa at (-5.32, 29.28, -14.00). (Replacing solvent molecule) Placed Cl- in aa at (-3.60, 28.55, -16.52). (Replacing solvent molecule) Placed Na+ in aa at (13.15, 31.53, -3.48). (Replacing solvent molecule) Placed Cl- in aa at (15.43, 31.60, -6.82). (Replacing solvent molecule) Placed Na+ in aa at (-0.71, 36.26, -19.73). (Replacing solvent molecule) Placed Cl- in aa at (-0.36, 32.77, -20.59). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -51.87 45.37 44.05 43.88 sized: 86.36 84.56 76.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.63% of box, grid points 118059 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 137 sec (Replacing solvent molecule) Placed Na+ in aa at (-3.35, 29.72, -19.90). (Replacing solvent molecule) Placed Cl- in aa at (-7.44, 27.59, -32.64). (Replacing solvent molecule) Placed Na+ in aa at (-4.09, 29.43, -29.45). (Replacing solvent molecule) Placed Cl- in aa at (-1.60, 28.96, -31.76). (Replacing solvent molecule) Placed Na+ in aa at (-3.77, 24.99, -35.03). (Replacing solvent molecule) Placed Cl- in aa at (-3.02, 27.44, -36.21). (Replacing solvent molecule) Placed Na+ in aa at (-0.12, 29.59, -35.83). (Replacing solvent molecule) Placed Cl- in aa at (0.13, 22.28, -36.76). (Replacing solvent molecule) Placed Na+ in aa at (2.46, 24.13, -37.43). (Replacing solvent molecule) Placed Cl- in aa at (-2.73, 26.01, -22.85). (Replacing solvent molecule) Placed Na+ in aa at (-7.50, 24.71, -26.06). (No solvent overlap) Placed Cl- in aa at (3.36, 25.56, -40.87). (Replacing solvent molecule) Placed Na+ in aa at (-6.25, 23.94, -20.10). (Replacing solvent molecule) Placed Cl- in aa at (-8.53, 23.87, -16.76). (Replacing solvent molecule) Placed Na+ in aa at (-11.11, 27.66, -16.38). (Replacing solvent molecule) Placed Cl- in aa at (-9.25, 25.96, -22.72). (Replacing solvent molecule) Placed Na+ in aa at (-9.77, 21.43, -16.10). (Replacing solvent molecule) Placed Cl- in aa at (-11.88, 22.68, -14.51). (Replacing solvent molecule) Placed Na+ in aa at (-15.40, 20.15, -12.26). (Replacing solvent molecule) Placed Cl- in aa at (-16.63, 22.84, -11.78). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -51.87 45.37 44.05 43.88 sized: 86.36 84.56 76.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.69% of box, grid points 119404 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 139 sec (Replacing solvent molecule) Placed Na+ in aa at (34.37, 14.10, 19.17). (Replacing solvent molecule) Placed Cl- in aa at (29.25, 12.31, 20.50). (Replacing solvent molecule) Placed Na+ in aa at (27.04, 9.28, 23.73). (Replacing solvent molecule) Placed Cl- in aa at (29.17, 6.73, 19.93). (Replacing solvent molecule) Placed Na+ in aa at (31.53, 5.94, 20.89). (Replacing solvent molecule) Placed Cl- in aa at (24.92, 9.72, 27.42). (Replacing solvent molecule) Placed Na+ in aa at (23.50, 12.62, 23.53). (Replacing solvent molecule) Placed Cl- in aa at (36.39, 0.75, 22.61). (Replacing solvent molecule) Placed Na+ in aa at (36.88, 3.20, 20.38). (Replacing solvent molecule) Placed Cl- in aa at (35.34, 6.89, 18.07). (Replacing solvent molecule) Placed Na+ in aa at (35.92, -3.07, 20.46). (Replacing solvent molecule) Placed Cl- in aa at (34.71, -5.10, 22.92). (Replacing solvent molecule) Placed Na+ in aa at (32.82, -6.32, 24.39). (Replacing solvent molecule) Placed Cl- in aa at (36.98, -9.74, 21.64). (Replacing solvent molecule) Placed Na+ in aa at (38.53, -12.19, 22.15). (Replacing solvent molecule) Placed Cl- in aa at (31.29, 3.70, 25.27). (Replacing solvent molecule) Placed Na+ in aa at (35.82, 0.46, 25.82). (Replacing solvent molecule) Placed Cl- in aa at (35.73, 1.28, 17.84). (Replacing solvent molecule) Placed Na+ in aa at (38.39, 8.37, 17.90). (Replacing solvent molecule) Placed Cl- in aa at (35.86, 17.05, 13.77). Done adding ions. >> addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -41.64 -43.44 -51.87 46.32 44.05 43.88 sized: 86.36 84.56 76.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.78% of box, grid points 121230 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 143 sec (Replacing solvent molecule) Placed Na+ in aa at (33.08, 17.64, 13.89). (Replacing solvent molecule) Placed Cl- in aa at (37.17, 11.67, 21.36). (Replacing solvent molecule) Placed Na+ in aa at (35.46, 7.88, 21.86). (Replacing solvent molecule) Placed Cl- in aa at (39.94, 5.41, 19.09). (Replacing solvent molecule) Placed Na+ in aa at (42.39, 9.16, 18.16). (Replacing solvent molecule) Placed Cl- in aa at (-8.19, 31.59, -17.14). (Replacing solvent molecule) Placed Na+ in aa at (-9.06, 26.85, -14.99). (Replacing solvent molecule) Placed Cl- in aa at (-11.43, 30.40, -12.94). (Replacing solvent molecule) Placed Na+ in aa at (-7.59, 32.71, -12.40). (Replacing solvent molecule) Placed Cl- in aa at (-6.71, 23.36, -30.13). (Replacing solvent molecule) Placed Na+ in aa at (-9.22, 20.18, -32.32). (Replacing solvent molecule) Placed Cl- in aa at (-10.43, 17.78, -33.35). (Replacing solvent molecule) Placed Na+ in aa at (-9.20, 17.18, -36.97). (Replacing solvent molecule) Placed Cl- in aa at (31.75, 24.25, 10.75). (Replacing solvent molecule) Placed Na+ in aa at (34.52, 23.34, 6.88). (Replacing solvent molecule) Placed Cl- in aa at (36.38, 21.36, 3.01). (Replacing solvent molecule) Placed Na+ in aa at (32.49, 21.49, 7.72). (Replacing solvent molecule) Placed Cl- in aa at (34.30, 20.66, 9.63). (Replacing solvent molecule) Placed Na+ in aa at (39.26, 21.77, 10.38). (Replacing solvent molecule) Placed Cl- in aa at (38.21, 23.53, 6.56). Done adding ions. >> >> saveamberparm aa 2BDM_cpz.topo 2BDM_cpz.coords Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1578 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CHIE 1 CPZ 1 HEM 1 NGLY 1 WAT 14871 ) (no restraints) > > quit Quit