log started: Thu Oct 6 23:27:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.spce ----- Source: /home/cerutti/AmberReload/dat/leap/cmd/leaprc.water.spce ----- Source of /home/cerutti/AmberReload/dat/leap/cmd/leaprc.water.spce done >> # >> # Load water and ions for SPC/E + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> addAtomTypes { >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = SPC >> WAT = SPC >> loadAmberParams frcmod.spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.spce Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for SPC/E water >> loadAmberParams frcmod.ionsjc_spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ionsjc_spce Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and SPC/E water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ions234lm_126_spce Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for SPC/E water model (12-6 normal usage set) >> > > fasciculin = loadPdb "1fsc_mod.pdb" Loading PDB file: ./1fsc_mod.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue THR, term: Terminal/beginning, seq. number: 0 to: NTHR. (Residue 1: MET, Nonterminal, was not found in name map.) (Residue 2: CYX, Nonterminal, was not found in name map.) (Residue 3: TYR, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: HIS, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: THR, Nonterminal, was not found in name map.) (Residue 9: SER, Nonterminal, was not found in name map.) (Residue 10: ARG, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: ILE, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: ASN, Nonterminal, was not found in name map.) (Residue 16: CYX, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: GLU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: CYX, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: ARG, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: SER, Nonterminal, was not found in name map.) (Residue 26: ARG, Nonterminal, was not found in name map.) (Residue 27: ARG, Nonterminal, was not found in name map.) (Residue 28: HIS, Nonterminal, was not found in name map.) (Residue 29: PRO, Nonterminal, was not found in name map.) (Residue 30: PRO, Nonterminal, was not found in name map.) (Residue 31: LYS, Nonterminal, was not found in name map.) (Residue 32: MET, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: LEU, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: ARG, Nonterminal, was not found in name map.) (Residue 37: GLY, Nonterminal, was not found in name map.) (Residue 38: CYX, Nonterminal, was not found in name map.) (Residue 39: GLY, Nonterminal, was not found in name map.) (Residue 40: CYX, Nonterminal, was not found in name map.) (Residue 41: PRO, Nonterminal, was not found in name map.) (Residue 42: PRO, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: ASP, Nonterminal, was not found in name map.) (Residue 45: ASP, Nonterminal, was not found in name map.) (Residue 46: ASN, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: GLU, Nonterminal, was not found in name map.) (Residue 49: VAL, Nonterminal, was not found in name map.) (Residue 50: LYS, Nonterminal, was not found in name map.) (Residue 51: CYX, Nonterminal, was not found in name map.) (Residue 52: CYX, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: PRO, Nonterminal, was not found in name map.) (Residue 56: ASP, Nonterminal, was not found in name map.) (Residue 57: LYS, Nonterminal, was not found in name map.) (Residue 58: CYX, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) Mapped residue TYR, term: Terminal/last, seq. number: 60 to: CTYR. (Residue 61: HOH, Terminal/beginning, was not found in name map.) (Residue 62: HOH, Nonterminal, was not found in name map.) (Residue 63: HOH, Nonterminal, was not found in name map.) (Residue 64: HOH, Nonterminal, was not found in name map.) (Residue 65: HOH, Nonterminal, was not found in name map.) (Residue 66: HOH, Nonterminal, was not found in name map.) (Residue 67: HOH, Nonterminal, was not found in name map.) (Residue 68: HOH, Nonterminal, was not found in name map.) (Residue 69: HOH, Nonterminal, was not found in name map.) (Residue 70: HOH, Nonterminal, was not found in name map.) (Residue 71: HOH, Nonterminal, was not found in name map.) (Residue 72: HOH, Nonterminal, was not found in name map.) (Residue 73: HOH, Nonterminal, was not found in name map.) (Residue 74: HOH, Nonterminal, was not found in name map.) (Residue 75: HOH, Nonterminal, was not found in name map.) (Residue 76: HOH, Nonterminal, was not found in name map.) (Residue 77: HOH, Nonterminal, was not found in name map.) (Residue 78: HOH, Nonterminal, was not found in name map.) (Residue 79: HOH, Nonterminal, was not found in name map.) (Residue 80: HOH, Nonterminal, was not found in name map.) (Residue 81: HOH, Nonterminal, was not found in name map.) (Residue 82: HOH, Nonterminal, was not found in name map.) (Residue 83: HOH, Nonterminal, was not found in name map.) (Residue 84: HOH, Nonterminal, was not found in name map.) (Residue 85: HOH, Nonterminal, was not found in name map.) (Residue 86: HOH, Nonterminal, was not found in name map.) (Residue 87: HOH, Nonterminal, was not found in name map.) (Residue 88: HOH, Nonterminal, was not found in name map.) (Residue 89: HOH, Nonterminal, was not found in name map.) (Residue 90: HOH, Nonterminal, was not found in name map.) (Residue 91: HOH, Nonterminal, was not found in name map.) (Residue 92: HOH, Nonterminal, was not found in name map.) (Residue 93: HOH, Nonterminal, was not found in name map.) (Residue 94: HOH, Nonterminal, was not found in name map.) (Residue 95: HOH, Nonterminal, was not found in name map.) (Residue 96: HOH, Nonterminal, was not found in name map.) (Residue 97: HOH, Nonterminal, was not found in name map.) (Residue 98: HOH, Nonterminal, was not found in name map.) (Residue 99: HOH, Nonterminal, was not found in name map.) (Residue 100: HOH, Nonterminal, was not found in name map.) (Residue 101: HOH, Nonterminal, was not found in name map.) (Residue 102: HOH, Nonterminal, was not found in name map.) (Residue 103: HOH, Nonterminal, was not found in name map.) (Residue 104: HOH, Nonterminal, was not found in name map.) (Residue 105: HOH, Nonterminal, was not found in name map.) (Residue 106: HOH, Nonterminal, was not found in name map.) (Residue 107: HOH, Nonterminal, was not found in name map.) (Residue 108: HOH, Nonterminal, was not found in name map.) (Residue 109: HOH, Nonterminal, was not found in name map.) (Residue 110: HOH, Nonterminal, was not found in name map.) (Residue 111: HOH, Nonterminal, was not found in name map.) (Residue 112: HOH, Nonterminal, was not found in name map.) (Residue 113: HOH, Nonterminal, was not found in name map.) (Residue 114: HOH, Nonterminal, was not found in name map.) (Residue 115: HOH, Terminal/last, was not found in name map.) Joining NTHR - MET Joining MET - CYX Joining CYX - TYR Joining TYR - SER Joining SER - HIE Joining HIE - THR Joining THR - THR Joining THR - THR Joining THR - SER Joining SER - ARG Joining ARG - ALA Joining ALA - ILE Joining ILE - LEU Joining LEU - THR Joining THR - ASN Joining ASN - CYX Joining CYX - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - SER Joining SER - CYX Joining CYX - TYR Joining TYR - ARG Joining ARG - LYS Joining LYS - SER Joining SER - ARG Joining ARG - ARG Joining ARG - HIE Joining HIE - PRO Joining PRO - PRO Joining PRO - LYS Joining LYS - MET Joining MET - VAL Joining VAL - LEU Joining LEU - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - CYX Joining CYX - GLY Joining GLY - CYX Joining CYX - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - ASP Joining ASP - ASP Joining ASP - ASN Joining ASN - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - CYX Joining CYX - CYX Joining CYX - THR Joining THR - SER Joining SER - PRO Joining PRO - ASP Joining ASP - LYS Joining LYS - CYX Joining CYX - ASN Joining ASN - CTYR Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC total atoms in file: 519 Leap added 552 missing atoms according to residue templates: 552 H / lone pairs > solvateOct fasciculin SPCBOX 14.0 Scaling up box by a factor of 1.333453 to meet diagonal cut criterion Solute vdw bounding box: 34.839 25.077 41.462 Total bounding box for atom centers: 78.799 78.799 78.799 (box expansion for 'iso' is 37.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 254071.479 A^3 (oct) Total mass 136036.592 amu, Density 0.889 g/cc Added 7121 residues. > addIons fasciculin Cl- 4 Adding 4 counter ions to "fasciculin" using 1A grid Total solute charge: 4.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.71 to 8.71 Box: enclosing: -29.08 -23.47 -23.72 23.01 28.65 23.56 sized: 34.92 40.53 40.28 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 10.16% of box, grid points 26644 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Cl- in fasciculin at (0.48, -0.41, -16.62). (Replacing solvent molecule) Placed Cl- in fasciculin at (-5.93, 5.45, 6.55). (Replacing solvent molecule) Placed Cl- in fasciculin at (11.15, 8.39, -9.91). (Replacing solvent molecule) Placed Cl- in fasciculin at (0.87, -16.93, -4.33). Done adding ions. > saveAmberParm fasciculin solvated_1fsc.top solvated_1fsc.crd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 180 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 CTYR 1 NTHR 1 WAT 7172 ) (no restraints) > quit Quit log started: Fri Oct 7 15:37:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.spce ----- Source: /home/cerutti/AmberReload/dat/leap/cmd/leaprc.water.spce ----- Source of /home/cerutti/AmberReload/dat/leap/cmd/leaprc.water.spce done >> # >> # Load water and ions for SPC/E + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> addAtomTypes { >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /home/cerutti/AmberReload/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = SPC >> WAT = SPC >> loadAmberParams frcmod.spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.spce Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for SPC/E water >> loadAmberParams frcmod.ionsjc_spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ionsjc_spce Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and SPC/E water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_spce Loading parameters: /home/cerutti/AmberReload/dat/leap/parm/frcmod.ions234lm_126_spce Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for SPC/E water model (12-6 normal usage set) >> > > fasciculin = loadPdb "1fsc_amb.pdb" Loading PDB file: ./1fsc_amb.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue THR, term: Terminal/beginning, seq. number: 0 to: NTHR. (Residue 1: MET, Nonterminal, was not found in name map.) (Residue 2: CYX, Nonterminal, was not found in name map.) (Residue 3: TYR, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: HIS, Nonterminal, was not found in name map.) (Residue 6: THR, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: THR, Nonterminal, was not found in name map.) (Residue 9: SER, Nonterminal, was not found in name map.) (Residue 10: ARG, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: ILE, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: ASN, Nonterminal, was not found in name map.) (Residue 16: CYX, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: GLU, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: CYX, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: ARG, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: SER, Nonterminal, was not found in name map.) (Residue 26: ARG, Nonterminal, was not found in name map.) (Residue 27: ARG, Nonterminal, was not found in name map.) (Residue 28: HIS, Nonterminal, was not found in name map.) (Residue 29: PRO, Nonterminal, was not found in name map.) (Residue 30: PRO, Nonterminal, was not found in name map.) (Residue 31: LYS, Nonterminal, was not found in name map.) (Residue 32: MET, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: LEU, Nonterminal, was not found in name map.) (Residue 35: GLY, Nonterminal, was not found in name map.) (Residue 36: ARG, Nonterminal, was not found in name map.) (Residue 37: GLY, Nonterminal, was not found in name map.) (Residue 38: CYX, Nonterminal, was not found in name map.) (Residue 39: GLY, Nonterminal, was not found in name map.) (Residue 40: CYX, Nonterminal, was not found in name map.) (Residue 41: PRO, Nonterminal, was not found in name map.) (Residue 42: PRO, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: ASP, Nonterminal, was not found in name map.) (Residue 45: ASP, Nonterminal, was not found in name map.) (Residue 46: ASN, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: GLU, Nonterminal, was not found in name map.) (Residue 49: VAL, Nonterminal, was not found in name map.) (Residue 50: LYS, Nonterminal, was not found in name map.) (Residue 51: CYX, Nonterminal, was not found in name map.) (Residue 52: CYX, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: SER, Nonterminal, was not found in name map.) (Residue 55: PRO, Nonterminal, was not found in name map.) (Residue 56: ASP, Nonterminal, was not found in name map.) (Residue 57: LYS, Nonterminal, was not found in name map.) (Residue 58: CYX, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) Mapped residue TYR, term: Terminal/last, seq. number: 60 to: CTYR. (Residue 61: HOH, Terminal/beginning, was not found in name map.) (Residue 62: HOH, Nonterminal, was not found in name map.) (Residue 63: HOH, Nonterminal, was not found in name map.) (Residue 64: HOH, Nonterminal, was not found in name map.) (Residue 65: HOH, Nonterminal, was not found in name map.) (Residue 66: HOH, Nonterminal, was not found in name map.) (Residue 67: HOH, Nonterminal, was not found in name map.) (Residue 68: HOH, Nonterminal, was not found in name map.) (Residue 69: HOH, Nonterminal, was not found in name map.) (Residue 70: HOH, Nonterminal, was not found in name map.) (Residue 71: HOH, Nonterminal, was not found in name map.) (Residue 72: HOH, Nonterminal, was not found in name map.) (Residue 73: HOH, Nonterminal, was not found in name map.) (Residue 74: HOH, Nonterminal, was not found in name map.) (Residue 75: HOH, Nonterminal, was not found in name map.) (Residue 76: HOH, Nonterminal, was not found in name map.) (Residue 77: HOH, Nonterminal, was not found in name map.) (Residue 78: HOH, Nonterminal, was not found in name map.) (Residue 79: HOH, Nonterminal, was not found in name map.) (Residue 80: HOH, Nonterminal, was not found in name map.) (Residue 81: HOH, Nonterminal, was not found in name map.) (Residue 82: HOH, Nonterminal, was not found in name map.) (Residue 83: HOH, Nonterminal, was not found in name map.) (Residue 84: HOH, Nonterminal, was not found in name map.) (Residue 85: HOH, Nonterminal, was not found in name map.) (Residue 86: HOH, Nonterminal, was not found in name map.) (Residue 87: HOH, Nonterminal, was not found in name map.) (Residue 88: HOH, Nonterminal, was not found in name map.) (Residue 89: HOH, Nonterminal, was not found in name map.) (Residue 90: HOH, Nonterminal, was not found in name map.) (Residue 91: HOH, Nonterminal, was not found in name map.) (Residue 92: HOH, Nonterminal, was not found in name map.) (Residue 93: HOH, Nonterminal, was not found in name map.) (Residue 94: HOH, Nonterminal, was not found in name map.) (Residue 95: HOH, Nonterminal, was not found in name map.) (Residue 96: HOH, Nonterminal, was not found in name map.) (Residue 97: HOH, Nonterminal, was not found in name map.) (Residue 98: HOH, Nonterminal, was not found in name map.) (Residue 99: HOH, Nonterminal, was not found in name map.) (Residue 100: HOH, Nonterminal, was not found in name map.) (Residue 101: HOH, Nonterminal, was not found in name map.) (Residue 102: HOH, Nonterminal, was not found in name map.) (Residue 103: HOH, Nonterminal, was not found in name map.) (Residue 104: HOH, Nonterminal, was not found in name map.) (Residue 105: HOH, Nonterminal, was not found in name map.) (Residue 106: HOH, Nonterminal, was not found in name map.) (Residue 107: HOH, Nonterminal, was not found in name map.) (Residue 108: HOH, Nonterminal, was not found in name map.) (Residue 109: HOH, Nonterminal, was not found in name map.) (Residue 110: HOH, Nonterminal, was not found in name map.) (Residue 111: HOH, Nonterminal, was not found in name map.) (Residue 112: HOH, Nonterminal, was not found in name map.) (Residue 113: HOH, Nonterminal, was not found in name map.) (Residue 114: HOH, Nonterminal, was not found in name map.) (Residue 115: HOH, Terminal/last, was not found in name map.) Joining NTHR - MET Joining MET - CYX Joining CYX - TYR Joining TYR - SER Joining SER - HIE Joining HIE - THR Joining THR - THR Joining THR - THR Joining THR - SER Joining SER - ARG Joining ARG - ALA Joining ALA - ILE Joining ILE - LEU Joining LEU - THR Joining THR - ASN Joining ASN - CYX Joining CYX - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - SER Joining SER - CYX Joining CYX - TYR Joining TYR - ARG Joining ARG - LYS Joining LYS - SER Joining SER - ARG Joining ARG - ARG Joining ARG - HIE Joining HIE - PRO Joining PRO - PRO Joining PRO - LYS Joining LYS - MET Joining MET - VAL Joining VAL - LEU Joining LEU - GLY Joining GLY - ARG Joining ARG - GLY Joining GLY - CYX Joining CYX - GLY Joining GLY - CYX Joining CYX - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - ASP Joining ASP - ASP Joining ASP - ASN Joining ASN - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - CYX Joining CYX - CYX Joining CYX - THR Joining THR - SER Joining SER - PRO Joining PRO - ASP Joining ASP - LYS Joining LYS - CYX Joining CYX - ASN Joining ASN - CTYR Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC Starting new chain with SPC total atoms in file: 519 Leap added 552 missing atoms according to residue templates: 552 H / lone pairs > solvateOct fasciculin SPCBOX 14.0 Scaling up box by a factor of 1.333453 to meet diagonal cut criterion Solute vdw bounding box: 34.839 25.077 41.462 Total bounding box for atom centers: 78.799 78.799 78.799 (box expansion for 'iso' is 37.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Volume: 254071.479 A^3 (oct) Total mass 136036.592 amu, Density 0.889 g/cc Added 7121 residues. > addIons fasciculin Cl- 4 Adding 4 counter ions to "fasciculin" using 1A grid Total solute charge: 4.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.71 to 8.71 Box: enclosing: -29.08 -23.47 -23.72 23.01 28.65 23.56 sized: 34.92 40.53 40.28 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 10.16% of box, grid points 26644 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Cl- in fasciculin at (0.48, -0.41, -16.62). (Replacing solvent molecule) Placed Cl- in fasciculin at (-5.93, 5.45, 6.55). (Replacing solvent molecule) Placed Cl- in fasciculin at (11.15, 8.39, -9.91). (Replacing solvent molecule) Placed Cl- in fasciculin at (0.87, -16.93, -4.33). Done adding ions. > saveAmberParm fasciculin solvated_1fsc.top solvated_1fsc.crd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 180 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 CTYR 1 NTHR 1 WAT 7172 ) (no restraints) > quit Quit