log started: Fri Aug 3 11:39:21 2007 Log file: ./leap.log > # > # ----- leaprc for loading the parm99 additive force field, no lone pairs > # assumes that any unspecified nucleic acids are DNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber9/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) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries. > # > loadOff all_amino94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > > loadOff ions94.lib Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > source leaprc.gaff ----- Source: /usr/local/amber9/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber9/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Aug 3 11:39:42 2007 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber9/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > loadamberparm ax_mecyclhex.prepin ERROR: syntax error log started: Fri Aug 3 11:41:14 2007 Log file: ./leap.log > # > # ----- leaprc for loading the parm99 additive force field, no lone pairs > # assumes that any unspecified nucleic acids are DNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber9/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) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries. > # > loadOff all_amino94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > > loadOff ions94.lib Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > source leaprc.gaff ----- Source: /usr/local/amber9/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber9/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Aug 3 11:41:31 2007 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber9/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > loadamberprep ax_mecyclhex.prepin Loading Prep file: ./ax_mecyclhex.prepin Loaded UNIT: AME > check AME Checking 'AME'.... Checking parameters for unit 'AME'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > solvatebox AME chcl3box 15 solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox AME chcl3box 15 solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvatebox AME CHCL3BOX 15 Solute vdw bounding box: 7.563 7.914 6.786 Total bounding box for atom centers: 37.563 37.914 36.786 Solvent unit box: 56.496 56.496 56.496 The number of boxes: x= 1 y= 1 z= 1 Adding box at: x=0 y=0 z=0 Center of solvent box is: 0.000000, 0.000000, 0.000000 (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) (using default radius 1.500000 for CL1) (using default radius 1.500000 for CL2) (using default radius 1.500000 for CL3) Total vdw box size: 40.349 40.825 39.450 angstroms. Volume: 64983.931 A^3 Mass > 4368.086 amu, Density > 0.112 g/cc (type - hence mass - of one or more atoms could not be found) Added 328 residues.