log started: Mon Jun 4 17:42:38 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # 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" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "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" } >>> { "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" "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" } >>> { "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" } >>> { "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" } >>> # glycam >>> { "OG" "O" "sp3" } >>> { "OL" "O" "sp3" } >>> { "AC" "C" "sp3" } >>> { "EC" "C" "sp3" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.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 aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.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 aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.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 nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX 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: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> 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 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 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" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = sequence { ACE AS4 NME } Sequence: ACE Sequence: AS4 Joining ACE - AS4 Sequence: NME Joining AS4 - NME > solvatebox system TIP3PBOX 12 0.75 Solute vdw bounding box: 9.871 10.680 5.995 Total bounding box for atom centers: 33.871 34.680 29.995 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Total vdw box size: 36.592 37.796 33.088 angstroms. Volume: 45761.414 A^3 Total mass 18207.210 amu, Density 0.661 g/cc Added 1000 residues. > saveamberparm system asp.prmtop asp.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1000 ) (no restraints) > > system = sequence { ACE GL4 NME } Sequence: ACE Sequence: GL4 Joining ACE - GL4 Sequence: NME Joining GL4 - NME > solvatebox system TIP3PBOX 12 0.75 Solute vdw bounding box: 10.407 10.679 7.642 Total bounding box for atom centers: 34.407 34.679 31.642 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Total vdw box size: 37.380 37.796 34.680 angstroms. Volume: 48996.963 A^3 Total mass 19752.596 amu, Density 0.669 g/cc Added 1085 residues. > saveamberparm system glu.prmtop glu.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1085 ) (no restraints) > > system = sequence { ACE HIP NME } Sequence: ACE Sequence: HIP Joining ACE - HIP Sequence: NME Joining HIP - NME > solvatebox system TIP3PBOX 12 0.75 Solute vdw bounding box: 11.179 10.679 6.640 Total bounding box for atom centers: 35.179 34.679 30.640 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Total vdw box size: 37.968 37.796 33.876 angstroms. Volume: 48612.997 A^3 Total mass 19542.418 amu, Density 0.668 g/cc Added 1073 residues. > saveamberparm system his.prmtop his.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 9 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1073 ) (no restraints) > > system = sequence { ACE LYS NME } Sequence: ACE Sequence: LYS Joining ACE - LYS Sequence: NME Joining LYS - NME > solvatebox system TIP3PBOX 12 0.75 Solute vdw bounding box: 11.785 10.679 7.778 Total bounding box for atom centers: 35.785 34.679 31.778 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Total vdw box size: 38.861 37.796 34.680 angstroms. Volume: 50937.523 A^3 Total mass 20668.456 amu, Density 0.674 g/cc Added 1136 residues. > saveamberparm system lys.prmtop lys.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 4 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1136 ) (no restraints) > > system = sequence { ACE TYR NME } Sequence: ACE Sequence: TYR Joining ACE - TYR Sequence: NME Joining TYR - NME > solvatebox system TIP3PBOX 12 0.75 Solute vdw bounding box: 12.424 10.679 6.894 Total bounding box for atom centers: 36.424 34.679 30.894 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Total vdw box size: 39.546 37.796 34.010 angstroms. Volume: 50833.943 A^3 Total mass 20594.348 amu, Density 0.673 g/cc Added 1130 residues. > saveamberparm system tyr.prmtop tyr.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 10 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1130 ) (no restraints) > > quit Quit