log started: Fri Aug 15 15:42:12 2008 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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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/chpc.utah.edu/common/home/u0181375/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 Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > 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 > > gaffnew = loadamberparams Tmx_gaff.dat Loading parameters: ./Tmx_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) > frcmod = loadamberparams Tmx_f.frcmod Loading parameters: ./Tmx_f.frcmod Reading force field modification type file (frcmod) Reading title: REMARK 8/6 Modified Junmei frcmod Unknown keyword: REMARK ca- in parameter file. > OHT = loadmol2 FOHT_1_RED_ac.mol2 Loading Mol2 file: ./FOHT_1_RED_ac.mol2 Reading MOLECULE named OHT > > aa = loadpdb b31.pdb Loading PDB file: ./b31.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, 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: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: LYS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) (Residue 473: OHT, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3874 Leap added 3938 missing atoms according to residue templates: 3908 H / lone pairs 30 unknown element > > bond aa.415.SG aa.473.FE > > saveamberparm aa b31_invacuo.topo b31_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: 3.000400 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 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1520 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 CTHR 1 HEM 1 NHIE 1 OHT 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.302791 to meet diagonal cut criterion Solute vdw bounding box: 46.866 77.717 63.235 Total bounding box for atom centers: 108.984 108.984 108.984 (box expansion for 'iso' is 60.9%) 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: 665202.476 A^3 (oct) Total mass 365354.982 amu, Density 0.912 g/cc Added 17225 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: -40.26 -42.40 -40.91 39.60 41.57 40.79 sized: 87.74 85.60 87.09 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.03% of box, grid points 84426 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 84 sec (Replacing solvent molecule) Placed Cl- in aa at (-22.41, -14.05, -7.10). (Replacing solvent molecule) Placed Cl- in aa at (-3.35, 29.80, 6.72). (Replacing solvent molecule) Placed Cl- in aa at (31.73, 0.34, 9.04). 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: -39.58 -41.72 -40.23 39.52 40.89 40.11 sized: 88.42 86.28 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.38% of box, grid points 91930 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 87 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.95, -31.92, -0.71). (Replacing solvent molecule) Placed Cl- in aa at (9.25, -1.62, 21.41). (Replacing solvent molecule) Placed Na+ in aa at (11.92, -4.10, 18.59). (Replacing solvent molecule) Placed Cl- in aa at (14.54, -3.32, 15.60). (Replacing solvent molecule) Placed Na+ in aa at (15.00, 1.03, 15.22). (Replacing solvent molecule) Placed Cl- in aa at (11.36, -4.69, 21.73). (Replacing solvent molecule) Placed Na+ in aa at (14.07, -1.15, 21.63). (Replacing solvent molecule) Placed Cl- in aa at (13.31, 0.59, 19.65). (Replacing solvent molecule) Placed Na+ in aa at (26.03, -4.69, -26.39). (Replacing solvent molecule) Placed Cl- in aa at (21.56, -8.66, -22.49). (Replacing solvent molecule) Placed Na+ in aa at (13.04, 10.31, 22.98). (No solvent overlap) Placed Cl- in aa at (17.42, 18.28, -22.23). (Replacing solvent molecule) Placed Na+ in aa at (-2.31, -27.99, -3.29). (Replacing solvent molecule) Placed Cl- in aa at (-9.01, -33.30, -2.95). (Replacing solvent molecule) Placed Na+ in aa at (-12.43, -32.28, -5.15). (Replacing solvent molecule) Placed Cl- in aa at (11.26, -20.47, 6.54). (Replacing solvent molecule) Placed Na+ in aa at (9.22, -21.57, 4.14). (Replacing solvent molecule) Placed Cl- in aa at (3.87, -24.55, 3.08). (Replacing solvent molecule) Placed Na+ in aa at (5.52, -24.30, -0.66). (Replacing solvent molecule) Placed Cl- in aa at (9.89, -24.45, 1.28). 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: -39.58 -41.72 -40.23 39.52 40.89 40.11 sized: 88.42 86.28 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.44% of box, grid points 93102 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 89 sec (Replacing solvent molecule) Placed Na+ in aa at (11.49, -24.90, -0.93). (Replacing solvent molecule) Placed Cl- in aa at (9.74, -27.46, -4.52). (Replacing solvent molecule) Placed Na+ in aa at (10.27, -29.53, -8.17). (Replacing solvent molecule) Placed Cl- in aa at (10.99, -33.87, -10.15). (Replacing solvent molecule) Placed Na+ in aa at (11.00, -36.92, -12.50). (Replacing solvent molecule) Placed Cl- in aa at (9.88, -36.75, -8.32). (Replacing solvent molecule) Placed Na+ in aa at (10.08, -29.33, -2.46). (Replacing solvent molecule) Placed Cl- in aa at (13.16, -37.38, -16.69). (Replacing solvent molecule) Placed Na+ in aa at (27.00, 9.29, 14.74). (Replacing solvent molecule) Placed Cl- in aa at (-21.94, -10.59, -3.04). (Replacing solvent molecule) Placed Na+ in aa at (-26.50, -12.12, -4.34). (Replacing solvent molecule) Placed Cl- in aa at (-28.05, -9.66, -4.85). (Replacing solvent molecule) Placed Na+ in aa at (-30.86, -7.87, -7.56). (Replacing solvent molecule) Placed Cl- in aa at (-29.31, -4.61, -9.15). (Replacing solvent molecule) Placed Na+ in aa at (-25.62, -0.78, -11.63). (Replacing solvent molecule) Placed Cl- in aa at (-27.41, 2.56, -10.29). (Replacing solvent molecule) Placed Na+ in aa at (-31.20, 2.60, -10.61). (Replacing solvent molecule) Placed Cl- in aa at (-25.19, -4.09, -13.07). (Replacing solvent molecule) Placed Na+ in aa at (-25.28, -4.96, -16.55). (Replacing solvent molecule) Placed Cl- in aa at (-19.77, 9.91, 20.28). 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: -39.58 -45.17 -40.23 39.52 40.89 40.11 sized: 88.42 82.83 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.61% of box, grid points 96761 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 90 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.74, -26.43, -1.22). (Replacing solvent molecule) Placed Cl- in aa at (14.11, -26.70, -0.67). (Replacing solvent molecule) Placed Na+ in aa at (13.59, -24.31, 4.17). (Replacing solvent molecule) Placed Cl- in aa at (-9.65, -28.38, 1.20). (Replacing solvent molecule) Placed Na+ in aa at (-8.01, -31.36, 4.86). (Replacing solvent molecule) Placed Cl- in aa at (3.87, 23.82, -17.15). (Replacing solvent molecule) Placed Na+ in aa at (-0.76, 24.32, -15.73). (Replacing solvent molecule) Placed Cl- in aa at (-6.24, 24.01, -20.03). (Replacing solvent molecule) Placed Na+ in aa at (5.70, 23.60, -19.92). (Replacing solvent molecule) Placed Cl- in aa at (2.01, 23.41, -19.61). (Replacing solvent molecule) Placed Na+ in aa at (-4.03, 24.09, -21.42). (Replacing solvent molecule) Placed Cl- in aa at (0.65, 28.75, -14.20). (Replacing solvent molecule) Placed Na+ in aa at (4.69, 28.14, -17.46). (Replacing solvent molecule) Placed Cl- in aa at (7.43, 28.48, -20.67). (Replacing solvent molecule) Placed Na+ in aa at (-1.19, 22.19, -23.43). (Replacing solvent molecule) Placed Cl- in aa at (1.32, 25.59, -23.89). (Replacing solvent molecule) Placed Na+ in aa at (5.10, 25.55, -23.57). (Replacing solvent molecule) Placed Cl- in aa at (3.87, 21.44, -23.47). (Replacing solvent molecule) Placed Na+ in aa at (2.84, 15.22, -23.48). (Replacing solvent molecule) Placed Cl- in aa at (-0.22, 11.39, -25.41). 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: -39.58 -45.17 -40.23 39.52 40.89 40.11 sized: 88.42 82.83 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.73% of box, grid points 99229 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 94 sec (No solvent overlap) Placed Na+ in aa at (8.42, 13.83, 23.77). (Replacing solvent molecule) Placed Cl- in aa at (12.98, 17.85, 23.69). (Replacing solvent molecule) Placed Na+ in aa at (10.49, 25.18, 19.30). (Replacing solvent molecule) Placed Cl- in aa at (10.14, 28.67, 20.16). (Replacing solvent molecule) Placed Na+ in aa at (0.95, 3.41, -24.03). (Replacing solvent molecule) Placed Cl- in aa at (9.90, 26.61, 16.73). (Replacing solvent molecule) Placed Na+ in aa at (7.57, 27.71, 20.56). (Replacing solvent molecule) Placed Cl- in aa at (3.23, 29.51, 21.63). (Replacing solvent molecule) Placed Na+ in aa at (8.30, 29.04, 16.16). (Replacing solvent molecule) Placed Cl- in aa at (-3.62, 18.87, -23.09). (Replacing solvent molecule) Placed Na+ in aa at (-2.59, 15.30, -24.93). (Replacing solvent molecule) Placed Cl- in aa at (-0.98, 6.01, -32.14). (Replacing solvent molecule) Placed Na+ in aa at (-1.32, 11.00, -28.36). (Replacing solvent molecule) Placed Cl- in aa at (0.16, 16.73, -25.77). (Replacing solvent molecule) Placed Na+ in aa at (-1.22, 3.78, -27.77). (Replacing solvent molecule) Placed Cl- in aa at (-3.02, 4.52, -22.87). (Replacing solvent molecule) Placed Na+ in aa at (-7.43, 4.67, -19.30). (Replacing solvent molecule) Placed Cl- in aa at (-6.97, 6.11, -23.47). (Replacing solvent molecule) Placed Na+ in aa at (-3.77, 7.16, -21.87). (Replacing solvent molecule) Placed Cl- in aa at (-10.86, 6.24, -18.77). 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: -39.58 -45.17 -40.23 39.52 40.89 40.11 sized: 88.42 82.83 87.77 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.83% of box, grid points 101388 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 99 sec (Replacing solvent molecule) Placed Na+ in aa at (26.50, 15.38, -3.20). (Replacing solvent molecule) Placed Cl- in aa at (3.27, 3.96, -27.22). (Replacing solvent molecule) Placed Na+ in aa at (3.31, 0.54, -27.21). (Replacing solvent molecule) Placed Cl- in aa at (-0.76, 1.33, -29.01). (Replacing solvent molecule) Placed Na+ in aa at (0.96, -0.59, -28.01). (Replacing solvent molecule) Placed Cl- in aa at (1.79, -2.26, -30.13). (Replacing solvent molecule) Placed Na+ in aa at (2.01, 0.42, -32.89). (Replacing solvent molecule) Placed Cl- in aa at (6.65, 25.17, 20.86). (Replacing solvent molecule) Placed Na+ in aa at (-1.73, -4.46, -30.12). (Replacing solvent molecule) Placed Cl- in aa at (-2.64, -1.10, -32.52). (Replacing solvent molecule) Placed Na+ in aa at (7.24, 20.96, 23.37). (Replacing solvent molecule) Placed Cl- in aa at (23.58, 25.24, -6.27). (Replacing solvent molecule) Placed Na+ in aa at (24.51, 22.88, -10.21). (Replacing solvent molecule) Placed Cl- in aa at (26.14, 22.61, -12.50). (Replacing solvent molecule) Placed Na+ in aa at (24.00, 23.94, -16.69). (Replacing solvent molecule) Placed Cl- in aa at (-5.53, -16.44, -18.08). (Replacing solvent molecule) Placed Na+ in aa at (-6.24, -21.98, -20.03). (Replacing solvent molecule) Placed Cl- in aa at (-11.57, -21.71, -20.38). (Replacing solvent molecule) Placed Na+ in aa at (-11.22, -18.22, -21.75). (Replacing solvent molecule) Placed Cl- in aa at (-10.70, -15.97, -23.42). 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: -39.58 -45.17 -40.68 39.52 40.89 40.11 sized: 88.42 82.83 87.32 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.93% of box, grid points 103411 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 100 sec (Replacing solvent molecule) Placed Na+ in aa at (-4.13, -15.32, -22.72). (Replacing solvent molecule) Placed Cl- in aa at (-6.39, -19.54, -22.05). (Replacing solvent molecule) Placed Na+ in aa at (-6.49, -21.80, -23.57). (Replacing solvent molecule) Placed Cl- in aa at (-3.92, -24.04, -23.42). (Replacing solvent molecule) Placed Na+ in aa at (-4.96, -29.88, -21.86). (Replacing solvent molecule) Placed Cl- in aa at (-8.98, -24.15, -20.60). (Replacing solvent molecule) Placed Na+ in aa at (-13.38, -24.61, -23.66). (Replacing solvent molecule) Placed Cl- in aa at (-7.59, -36.20, 0.94). (Replacing solvent molecule) Placed Na+ in aa at (-4.55, -33.42, 1.08). (Replacing solvent molecule) Placed Cl- in aa at (-1.03, -30.90, -1.17). (Replacing solvent molecule) Placed Na+ in aa at (-12.28, -28.42, -17.89). (Replacing solvent molecule) Placed Cl- in aa at (-8.77, -24.28, -25.73). (Replacing solvent molecule) Placed Na+ in aa at (-5.73, -35.76, 2.98). (Replacing solvent molecule) Placed Cl- in aa at (-3.39, -36.75, -0.87). (Replacing solvent molecule) Placed Na+ in aa at (-5.47, -36.63, -2.75). (Replacing solvent molecule) Placed Cl- in aa at (-3.41, -32.83, 5.88). (Replacing solvent molecule) Placed Na+ in aa at (-2.64, -24.09, -19.24). (Replacing solvent molecule) Placed Cl- in aa at (-7.90, -30.37, -17.90). (Replacing solvent molecule) Placed Na+ in aa at (0.16, -29.25, 0.78). (Replacing solvent molecule) Placed Cl- in aa at (-1.10, -19.79, -17.80). 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: -39.58 -45.17 -40.68 39.52 40.89 40.11 sized: 88.42 82.83 87.32 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.02% of box, grid points 105264 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 102 sec (No solvent overlap) Placed Na+ in aa at (19.42, -0.17, -30.68). (Replacing solvent molecule) Placed Cl- in aa at (-14.10, -25.94, -19.26). (Replacing solvent molecule) Placed Na+ in aa at (-18.45, -24.14, -18.20). (Replacing solvent molecule) Placed Cl- in aa at (-21.01, -23.00, -13.78). (Replacing solvent molecule) Placed Na+ in aa at (-13.03, 8.62, -11.07). (Replacing solvent molecule) Placed Cl- in aa at (6.66, -9.04, 12.21). (Replacing solvent molecule) Placed Na+ in aa at (13.04, -12.69, 9.71). (Replacing solvent molecule) Placed Cl- in aa at (15.46, -12.16, 12.02). (Replacing solvent molecule) Placed Na+ in aa at (17.59, -8.81, 10.45). (Replacing solvent molecule) Placed Cl- in aa at (18.08, -6.11, 12.62). (Replacing solvent molecule) Placed Na+ in aa at (16.98, -2.72, 12.99). (Replacing solvent molecule) Placed Cl- in aa at (19.09, -12.64, 8.08). (Replacing solvent molecule) Placed Na+ in aa at (19.60, -4.48, 9.00). (Replacing solvent molecule) Placed Cl- in aa at (21.41, -1.37, 11.08). (Replacing solvent molecule) Placed Na+ in aa at (25.66, -0.31, 12.26). (Replacing solvent molecule) Placed Cl- in aa at (15.21, -4.39, 7.17). (Replacing solvent molecule) Placed Na+ in aa at (8.65, -6.71, 15.48). (Replacing solvent molecule) Placed Cl- in aa at (7.32, -4.09, 13.48). (Replacing solvent molecule) Placed Na+ in aa at (9.62, -3.89, 12.06). (Replacing solvent molecule) Placed Cl- in aa at (8.35, -7.62, 19.45). Done adding ions. > > saveamberparm aa b31.topo b31.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 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1520 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 CTHR 1 HEM 1 NHIE 1 OHT 1 WAT 17085 ) (no restraints) > > quit Quit