log started: Thu Jul 4 11:40:20 2019 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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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" "HYP" } { 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.tip3p ----- Source: /opt/software/amber/16/dat/leap/cmd/leaprc.water.tip3p ----- Source of /opt/software/amber/16/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "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" } >> { "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: /opt/software/amber/16/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: /opt/software/amber/16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for SPC/E water >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > source leaprc.GLYCAM_06j-1 ----- Source: /opt/software/amber/16/dat/leap/cmd/leaprc.GLYCAM_06j-1 ----- Source of /opt/software/amber/16/dat/leap/cmd/leaprc.GLYCAM_06j-1 done >> # ----- leaprc for loading the Glycam_06 carbohydrate force field >> # also contains atom types for lipids >> # >> # load atom type hybridizations >> # (includes atom types relevant to lipids) >> # >> addAtomTypes { >> { "C" "C" "sp2" } >> { "Cg" "C" "sp3" } >> { "Cy" "C" "sp3" } >> { "Ck" "C" "sp2" } >> { "CT" "C" "sp3" } >> { "Cj" "C" "sp2" } >> { "Cp" "C" "sp3" } >> { "H" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "Ha" "H" "sp3" } >> { "Hp" "H" "sp3" } >> { "Hc" "H" "sp3" } >> { "Ho" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "Ng" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "Oh" "O" "sp3" } >> { "Os" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "Oy" "O" "sp3" } >> { "S" "S" "sp3" } >> { "Sm" "S" "sp3" } >> { "P" "P" "sp3" } >> } >> # >> # load the main paramter set >> # >> glycam_06 = loadamberparams GLYCAM_06j.dat Loading parameters: /opt/software/amber/16/dat/leap/parm/GLYCAM_06j.dat Reading title: GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011 >> ## >> # >> # load all prep files for polysaccharides >> # >> loadamberprep GLYCAM_06j-1.prep Loading Prep file: /opt/software/amber/16/dat/leap/prep/GLYCAM_06j-1.prep Loaded UNIT: 0AA Loaded UNIT: 0AB Loaded UNIT: 0AD Loaded UNIT: 0AE Loaded UNIT: 0AF Loaded UNIT: 0AU Loaded UNIT: 0BA Loaded UNIT: 0BB Loaded UNIT: 0BC Loaded UNIT: 0BD Loaded UNIT: 0BU Loaded UNIT: 0CA Loaded UNIT: 0CB Loaded UNIT: 0CD Loaded UNIT: 0CU Loaded UNIT: 0DA Loaded UNIT: 0DB Loaded UNIT: 0DD Loaded UNIT: 0DU Loaded UNIT: 0EA Loaded UNIT: 0EB Loaded UNIT: 0FA Loaded UNIT: 0FB Loaded UNIT: 0GA Loaded UNIT: 0GB Loaded UNIT: 0GL Loaded UNIT: 0HA Loaded UNIT: 0HB Loaded UNIT: 0JA Loaded UNIT: 0JB Loaded UNIT: 0JD Loaded UNIT: 0JU Loaded UNIT: 0KA Loaded UNIT: 0KB Loaded UNIT: 0LA Loaded UNIT: 0LB Loaded UNIT: 0MA Loaded UNIT: 0MB Loaded UNIT: 0NA Loaded UNIT: 0NB Loaded UNIT: 0OA Loaded UNIT: 0OB Loaded UNIT: 0PA Loaded UNIT: 0PB Loaded UNIT: 0PD Loaded UNIT: 0PU Loaded UNIT: 0QA Loaded UNIT: 0QB Loaded UNIT: 0RA Loaded UNIT: 0RB Loaded UNIT: 0RD Loaded UNIT: 0RU Loaded UNIT: 0SA Loaded UNIT: 0SB Loaded UNIT: 0TA Loaded UNIT: 0TB Loaded UNIT: 0TV Loaded UNIT: 0Tv Loaded UNIT: 0UA Loaded UNIT: 0UB Loaded UNIT: 0VA Loaded UNIT: 0VB Loaded UNIT: 0WA Loaded UNIT: 0WB Loaded UNIT: 0XA Loaded UNIT: 0XB Loaded UNIT: 0XD Loaded UNIT: 0XU Loaded UNIT: 0YA Loaded UNIT: 0YB Loaded UNIT: 0ZA Loaded UNIT: 0ZB Loaded UNIT: 0aA Loaded UNIT: 0aB Loaded UNIT: 0aD Loaded UNIT: 0aU Loaded UNIT: 0bA Loaded UNIT: 0bB Loaded UNIT: 0bC Loaded UNIT: 0bD Loaded UNIT: 0bU Loaded UNIT: 0cA Loaded UNIT: 0cB Loaded UNIT: 0cD Loaded UNIT: 0cU Loaded UNIT: 0dA Loaded UNIT: 0dB Loaded UNIT: 0dD Loaded UNIT: 0dR Loaded UNIT: 0dU Loaded UNIT: 0eA Loaded UNIT: 0eB Loaded UNIT: 0fA Loaded UNIT: 0fB Loaded UNIT: 0gA Loaded UNIT: 0gB Loaded UNIT: 0gL Loaded UNIT: 0hA Loaded UNIT: 0hB Loaded UNIT: 0jA Loaded UNIT: 0jB Loaded UNIT: 0jD Loaded UNIT: 0jU Loaded UNIT: 0kA Loaded UNIT: 0kB Loaded UNIT: 0lA Loaded UNIT: 0lB Loaded UNIT: 0mA Loaded UNIT: 0mB Loaded UNIT: 0nA Loaded UNIT: 0nB Loaded UNIT: 0oA Loaded UNIT: 0oB Loaded UNIT: 0pA Loaded UNIT: 0pB Loaded UNIT: 0pD Loaded UNIT: 0pU Loaded UNIT: 0qA Loaded UNIT: 0qB Loaded UNIT: 0rA Loaded UNIT: 0rB Loaded UNIT: 0rD Loaded UNIT: 0rU Loaded UNIT: 0sA Loaded UNIT: 0sB Loaded UNIT: 0tA Loaded UNIT: 0tB Loaded UNIT: 0tV Loaded UNIT: 0tv Loaded UNIT: 0uA Loaded UNIT: 0uB Loaded UNIT: 0vA Loaded UNIT: 0vB Loaded UNIT: 0wA Loaded UNIT: 0wB Loaded UNIT: 0xA Loaded UNIT: 0xB Loaded UNIT: 0xD Loaded UNIT: 0xU Loaded UNIT: 0yA Loaded UNIT: 0yB Loaded UNIT: 0zA Loaded UNIT: 0zB Loaded UNIT: 1AA Loaded UNIT: 1AB Loaded UNIT: 1AD Loaded UNIT: 1AU Loaded UNIT: 1BA Loaded UNIT: 1BB Loaded UNIT: 1BD Loaded UNIT: 1BU Loaded UNIT: 1CA Loaded UNIT: 1CB Loaded UNIT: 1CD Loaded UNIT: 1CU Loaded UNIT: 1DA Loaded UNIT: 1DB Loaded UNIT: 1DD Loaded UNIT: 1DU Loaded UNIT: 1EA Loaded UNIT: 1EB Loaded UNIT: 1FA Loaded UNIT: 1FB Loaded UNIT: 1GA Loaded UNIT: 1GB Loaded UNIT: 1HA Loaded UNIT: 1HB Loaded UNIT: 1JA Loaded UNIT: 1JB Loaded UNIT: 1JD Loaded UNIT: 1JU Loaded UNIT: 1KA Loaded UNIT: 1KB Loaded UNIT: 1LA Loaded UNIT: 1LB Loaded UNIT: 1MA Loaded UNIT: 1MB Loaded UNIT: 1NA Loaded UNIT: 1NB Loaded UNIT: 1OA Loaded UNIT: 1OB Loaded UNIT: 1PA Loaded UNIT: 1PB Loaded UNIT: 1PD Loaded UNIT: 1PU Loaded UNIT: 1QA Loaded UNIT: 1QB Loaded UNIT: 1RA Loaded UNIT: 1RB Loaded UNIT: 1RD Loaded UNIT: 1RU Loaded UNIT: 1TA Loaded UNIT: 1TB Loaded UNIT: 1TV Loaded UNIT: 1Tv Loaded UNIT: 1UA Loaded UNIT: 1UB Loaded UNIT: 1VA Loaded UNIT: 1VB Loaded UNIT: 1WA Loaded UNIT: 1WB Loaded UNIT: 1XA Loaded UNIT: 1XB Loaded UNIT: 1XD Loaded UNIT: 1XU Loaded UNIT: 1YA Loaded UNIT: 1YB Loaded UNIT: 1ZA Loaded UNIT: 1ZB Loaded UNIT: 1aA Loaded UNIT: 1aB Loaded UNIT: 1aD Loaded UNIT: 1aU Loaded UNIT: 1bA Loaded UNIT: 1bB Loaded UNIT: 1bD Loaded UNIT: 1bU Loaded UNIT: 1cA Loaded UNIT: 1cB Loaded UNIT: 1cD Loaded UNIT: 1cU Loaded UNIT: 1dA Loaded UNIT: 1dB Loaded UNIT: 1dD Loaded UNIT: 1dU Loaded UNIT: 1eA Loaded UNIT: 1eB Loaded UNIT: 1fA Loaded UNIT: 1fB Loaded UNIT: 1gA Loaded UNIT: 1gB Loaded UNIT: 1hA Loaded UNIT: 1hB Loaded UNIT: 1jA Loaded UNIT: 1jB Loaded UNIT: 1jD Loaded UNIT: 1jU Loaded UNIT: 1kA Loaded UNIT: 1kB Loaded UNIT: 1lA Loaded UNIT: 1lB Loaded UNIT: 1mA Loaded UNIT: 1mB Loaded UNIT: 1nA Loaded UNIT: 1nB Loaded UNIT: 1oA Loaded UNIT: 1oB Loaded UNIT: 1pA Loaded UNIT: 1pB Loaded UNIT: 1pD Loaded UNIT: 1pU Loaded UNIT: 1qA Loaded UNIT: 1qB Loaded UNIT: 1rA Loaded UNIT: 1rB Loaded UNIT: 1rD Loaded UNIT: 1rU Loaded UNIT: 1tA Loaded UNIT: 1tB Loaded UNIT: 1tV Loaded UNIT: 1tv Loaded UNIT: 1uA Loaded UNIT: 1uB Loaded UNIT: 1vA Loaded UNIT: 1vB Loaded UNIT: 1wA Loaded UNIT: 1wB Loaded UNIT: 1xA Loaded UNIT: 1xB Loaded UNIT: 1xD Loaded UNIT: 1xU Loaded UNIT: 1yA Loaded UNIT: 1yB Loaded UNIT: 1zA Loaded UNIT: 1zB Loaded UNIT: 2AA Loaded UNIT: 2AB Loaded UNIT: 2AD Loaded UNIT: 2AE Loaded UNIT: 2AF Loaded UNIT: 2AU Loaded UNIT: 2BA Loaded UNIT: 2BB Loaded UNIT: 2BD Loaded UNIT: 2BU Loaded UNIT: 2CA Loaded UNIT: 2CB Loaded UNIT: 2CD Loaded UNIT: 2CU Loaded UNIT: 2DA Loaded UNIT: 2DB Loaded UNIT: 2DD Loaded UNIT: 2DU Loaded UNIT: 2EA Loaded UNIT: 2EB Loaded UNIT: 2FA Loaded UNIT: 2FB Loaded UNIT: 2GA Loaded UNIT: 2GB Loaded UNIT: 2HA Loaded UNIT: 2HB Loaded UNIT: 2JA Loaded UNIT: 2JB Loaded UNIT: 2JD Loaded UNIT: 2JU Loaded UNIT: 2KA Loaded UNIT: 2KB Loaded UNIT: 2LA Loaded UNIT: 2LB Loaded UNIT: 2MA Loaded UNIT: 2MB Loaded UNIT: 2NA Loaded UNIT: 2NB Loaded UNIT: 2OA Loaded UNIT: 2OB Loaded UNIT: 2PA Loaded UNIT: 2PB Loaded UNIT: 2PD Loaded UNIT: 2PU Loaded UNIT: 2QA Loaded UNIT: 2QB Loaded UNIT: 2RA Loaded UNIT: 2RB Loaded UNIT: 2RD Loaded UNIT: 2RU Loaded UNIT: 2TA Loaded UNIT: 2TB Loaded UNIT: 2TV Loaded UNIT: 2Tv Loaded UNIT: 2UA Loaded UNIT: 2UB Loaded UNIT: 2XA Loaded UNIT: 2XB Loaded UNIT: 2XD Loaded UNIT: 2XU Loaded UNIT: 2ZA Loaded UNIT: 2ZB Loaded UNIT: 2aA Loaded UNIT: 2aB Loaded UNIT: 2aD Loaded UNIT: 2aU Loaded UNIT: 2bA Loaded UNIT: 2bB Loaded UNIT: 2bD Loaded UNIT: 2bU Loaded UNIT: 2cA Loaded UNIT: 2cB Loaded UNIT: 2cD Loaded UNIT: 2cU Loaded UNIT: 2dA Loaded UNIT: 2dB Loaded UNIT: 2dD Loaded UNIT: 2dU Loaded UNIT: 2eA Loaded UNIT: 2eB Loaded UNIT: 2fA Loaded UNIT: 2fB Loaded UNIT: 2gA Loaded UNIT: 2gB Loaded UNIT: 2hA Loaded UNIT: 2hB Loaded UNIT: 2jA Loaded UNIT: 2jB Loaded UNIT: 2jD Loaded UNIT: 2jU Loaded UNIT: 2kA Loaded UNIT: 2kB Loaded UNIT: 2lA Loaded UNIT: 2lB Loaded UNIT: 2mA Loaded UNIT: 2mB Loaded UNIT: 2nA Loaded UNIT: 2nB Loaded UNIT: 2oA Loaded UNIT: 2oB Loaded UNIT: 2pA Loaded UNIT: 2pB Loaded UNIT: 2pD Loaded UNIT: 2pU Loaded UNIT: 2qA Loaded UNIT: 2qB Loaded UNIT: 2rA Loaded UNIT: 2rB Loaded UNIT: 2rD Loaded UNIT: 2rU Loaded UNIT: 2tA Loaded UNIT: 2tB Loaded UNIT: 2tV Loaded UNIT: 2tv Loaded UNIT: 2uA Loaded UNIT: 2uB Loaded UNIT: 2xA Loaded UNIT: 2xB Loaded UNIT: 2xD Loaded UNIT: 2xU Loaded UNIT: 2zA Loaded UNIT: 2zB Loaded UNIT: 3AA Loaded UNIT: 3AB Loaded UNIT: 3AD Loaded UNIT: 3AU Loaded UNIT: 3BA Loaded UNIT: 3BB Loaded UNIT: 3BC Loaded UNIT: 3BD Loaded UNIT: 3BU Loaded UNIT: 3CA Loaded UNIT: 3CB Loaded UNIT: 3CD Loaded UNIT: 3CU Loaded UNIT: 3DA Loaded UNIT: 3DB Loaded UNIT: 3DD Loaded UNIT: 3DU Loaded UNIT: 3EA Loaded UNIT: 3EB Loaded UNIT: 3FA Loaded UNIT: 3FB Loaded UNIT: 3GA Loaded UNIT: 3GB Loaded UNIT: 3HA Loaded UNIT: 3HB Loaded UNIT: 3JA Loaded UNIT: 3JB Loaded UNIT: 3JD Loaded UNIT: 3JU Loaded UNIT: 3KA Loaded UNIT: 3KB Loaded UNIT: 3LA Loaded UNIT: 3LB Loaded UNIT: 3MA Loaded UNIT: 3MB Loaded UNIT: 3NA Loaded UNIT: 3NB Loaded UNIT: 3OA Loaded UNIT: 3OB Loaded UNIT: 3PA Loaded UNIT: 3PB Loaded UNIT: 3PD Loaded UNIT: 3PU Loaded UNIT: 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Loaded UNIT: WxA Loaded UNIT: WxB Loaded UNIT: WyA Loaded UNIT: WyB Loaded UNIT: WzA Loaded UNIT: WzB Loaded UNIT: XEA Loaded UNIT: XEB Loaded UNIT: XGA Loaded UNIT: XGB Loaded UNIT: XKA Loaded UNIT: XKB Loaded UNIT: XLA Loaded UNIT: XLB Loaded UNIT: XMA Loaded UNIT: XMB Loaded UNIT: XNA Loaded UNIT: XNB Loaded UNIT: XTA Loaded UNIT: XTB Loaded UNIT: XeA Loaded UNIT: XeB Loaded UNIT: XgA Loaded UNIT: XgB Loaded UNIT: XkA Loaded UNIT: XkB Loaded UNIT: XlA Loaded UNIT: XlB Loaded UNIT: XmA Loaded UNIT: XmB Loaded UNIT: XnA Loaded UNIT: XnB Loaded UNIT: XtA Loaded UNIT: XtB Loaded UNIT: YAA Loaded UNIT: YAB Loaded UNIT: YAF Loaded UNIT: YDA Loaded UNIT: YDB Loaded UNIT: YEA Loaded UNIT: YEB Loaded UNIT: YFA Loaded UNIT: YFB Loaded UNIT: YGA Loaded UNIT: YGB Loaded UNIT: YGa Loaded UNIT: YHA Loaded UNIT: YHB Loaded UNIT: YKA Loaded UNIT: YKB Loaded UNIT: YLA Loaded UNIT: YLB Loaded UNIT: YMA Loaded UNIT: YMB Loaded UNIT: YNA Loaded UNIT: YNB Loaded UNIT: YOA Loaded UNIT: YOB Loaded UNIT: YQA Loaded UNIT: YQB Loaded UNIT: YRA Loaded UNIT: YRB Loaded UNIT: YTA Loaded UNIT: YTB Loaded UNIT: YTV Loaded UNIT: YTv Loaded UNIT: YUA Loaded UNIT: YUB Loaded UNIT: YXA Loaded UNIT: YXB Loaded UNIT: YZA Loaded UNIT: YZB Loaded UNIT: YaA Loaded UNIT: YaB Loaded UNIT: YdA Loaded UNIT: YdB Loaded UNIT: YeA Loaded UNIT: YeB Loaded UNIT: YfA Loaded UNIT: YfB Loaded UNIT: YgA Loaded UNIT: YgB Loaded UNIT: YhA Loaded UNIT: YhB Loaded UNIT: YkA Loaded UNIT: YkB Loaded UNIT: YlA Loaded UNIT: YlB Loaded UNIT: YmA Loaded UNIT: YmB Loaded UNIT: YnA Loaded UNIT: YnB Loaded UNIT: YoA Loaded UNIT: YoB Loaded UNIT: YqA Loaded UNIT: YqB Loaded UNIT: YrA Loaded UNIT: YrB Loaded UNIT: YtA Loaded UNIT: YtB Loaded UNIT: YtV Loaded UNIT: Ytv Loaded UNIT: YuA Loaded UNIT: YuB Loaded UNIT: YxA Loaded UNIT: YxB Loaded UNIT: YzA Loaded UNIT: YzB Loaded UNIT: ZAA Loaded UNIT: ZAB Loaded UNIT: ZAD Loaded UNIT: ZAU Loaded UNIT: ZDA Loaded UNIT: ZDB Loaded UNIT: ZDD Loaded UNIT: ZDU Loaded UNIT: ZEA Loaded UNIT: ZEB Loaded UNIT: ZFA Loaded UNIT: ZFB Loaded UNIT: ZGA Loaded UNIT: ZGB Loaded UNIT: ZHA Loaded UNIT: ZHB Loaded UNIT: ZKA Loaded UNIT: ZKB Loaded UNIT: ZLA Loaded UNIT: ZLB Loaded UNIT: ZMA Loaded UNIT: ZMB Loaded UNIT: ZNA Loaded UNIT: ZNB Loaded UNIT: ZOA Loaded UNIT: ZOB Loaded UNIT: ZOLS Loaded UNIT: ZOLT Loaded UNIT: ZQA Loaded UNIT: ZQB Loaded UNIT: ZRA Loaded UNIT: ZRB Loaded UNIT: ZRD Loaded UNIT: ZRU Loaded UNIT: ZTA Loaded UNIT: ZTB Loaded UNIT: ZUA Loaded UNIT: ZUB Loaded UNIT: ZXA Loaded UNIT: ZXB Loaded UNIT: ZXD Loaded UNIT: ZXU Loaded UNIT: ZZA Loaded UNIT: ZZB Loaded UNIT: ZaA Loaded UNIT: ZaB Loaded UNIT: ZaD Loaded UNIT: ZaU Loaded UNIT: ZdA Loaded UNIT: ZdB Loaded UNIT: ZdD Loaded UNIT: ZdU Loaded UNIT: ZeA Loaded UNIT: ZeB Loaded UNIT: ZfA Loaded UNIT: ZfB Loaded UNIT: ZgA Loaded UNIT: ZgB Loaded UNIT: ZhA Loaded UNIT: ZhB Loaded UNIT: ZkA Loaded UNIT: ZkB Loaded UNIT: ZlA Loaded UNIT: ZlB Loaded UNIT: ZmA Loaded UNIT: ZmB Loaded UNIT: ZnA Loaded UNIT: ZnB Loaded UNIT: ZoA Loaded UNIT: ZoB Loaded UNIT: ZqA Loaded UNIT: ZqB Loaded UNIT: ZrA Loaded UNIT: ZrB Loaded UNIT: ZrD Loaded UNIT: ZrU Loaded UNIT: ZtA Loaded UNIT: ZtB Loaded UNIT: ZuA Loaded UNIT: ZuB Loaded UNIT: ZxA Loaded UNIT: ZxB Loaded UNIT: ZxD Loaded UNIT: ZxU Loaded UNIT: ZzA Loaded UNIT: ZzB >> # >> # load lib files >> # >> # for attaching glycans to proteins >> loadOff GLYCAM_amino_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_amino_06j_12SB.lib Loading: HYP Loading: NLN Loading: OLP Loading: OLS Loading: OLT >> loadOff GLYCAM_aminoct_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib Loading: CHYP Loading: CNLN Loading: COLP Loading: COLS Loading: COLT >> loadOff GLYCAM_aminont_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib Loading: NHYP Loading: NNLN Loading: NOLP Loading: NOLS Loading: NOLT >> ## add residue maps for linking glycans to proteins >> ## Note! use of these requires sourcing the ff12SB leaprc and loading the amino >> ## libraries commented out in the load libs section >> addPdbResMap { >> { 0 "OLS" "NOLS" } { 1 "OLS" "COLS" } >> { 0 "OLT" "NOLT" } { 1 "OLT" "COLT" } >> { 0 "OLP" "NOLP" } { 1 "OLP" "COLP" } >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "NLN" "NNLN" } { 1 "NLN" "CNLN" } >> } Substituting map 0HYP -> NHYP for 0HYP -> HYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP >> # >> # for explicit solvent and ions >> # >> # the following assumes most users want to use tip3p as the >> # explicit solvent model >> # this can easily switched by the following commands in leap: >> # WAT = TP5 >> # loadamberparams frcmod.tip5p >> # >> loadOff solvents.lib # solvents Loading library: /opt/software/amber/16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 # set default water model >> WAT = TP3 >> loadOff atomic_ions.lib # load ions library Loading library: /opt/software/amber/16/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 >> # to use ions for TIP5P, you will need to use a different frcmod below >> # If desired, see the AMBER manual for additional ion force field options. >> ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > g1dr9 = loadPdb "1dr9_charmmoutput_vmd.pdb" Could not open file 1dr9_charmmoutput_vmd.pdb: not found > bond g1dr9.16.SG g1dr9.82.SG bond: Argument #1 is type String must be of type: [atom] usage: bond [order] > bond g1dr9.128.SG g1dr9.182.SG bond: Argument #1 is type String must be of type: [atom] usage: bond [order] > solvateOct g1dr9 TIP3PBOX 14.0 solvateOct: Argument #1 is type String must be of type: [unit] usage: solvateOct [aniso] [closeness] > #addIons fasciculin Na+ 20 Cl- 24 > savepdb g1dr9 g1dr9_leap.pdb savePdb: Argument #1 is type String must be of type: [unit] usage: savePdb > saveAmberParm g1dr9 solvated_g1dr9.top solvated_g1dr9.crd saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > quit Quit log started: Thu Jul 4 11:43:40 2019 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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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: /opt/software/amber/16/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" "HYP" } { 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.tip3p ----- Source: /opt/software/amber/16/dat/leap/cmd/leaprc.water.tip3p ----- Source of /opt/software/amber/16/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "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" } >> { "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: /opt/software/amber/16/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: /opt/software/amber/16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for SPC/E water >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > source leaprc.GLYCAM_06j-1 ----- Source: /opt/software/amber/16/dat/leap/cmd/leaprc.GLYCAM_06j-1 ----- Source of /opt/software/amber/16/dat/leap/cmd/leaprc.GLYCAM_06j-1 done >> # ----- leaprc for loading the Glycam_06 carbohydrate force field >> # also contains atom types for lipids >> # >> # load atom type hybridizations >> # (includes atom types relevant to lipids) >> # >> addAtomTypes { >> { "C" "C" "sp2" } >> { "Cg" "C" "sp3" } >> { "Cy" "C" "sp3" } >> { "Ck" "C" "sp2" } >> { "CT" "C" "sp3" } >> { "Cj" "C" "sp2" } >> { "Cp" "C" "sp3" } >> { "H" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "Ha" "H" "sp3" } >> { "Hp" "H" "sp3" } >> { "Hc" "H" "sp3" } >> { "Ho" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "Ng" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "Oh" "O" "sp3" } >> { "Os" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "Oy" "O" "sp3" } >> { "S" "S" "sp3" } >> { "Sm" "S" "sp3" } >> { "P" "P" "sp3" } >> } >> # >> # load the main paramter set >> # >> glycam_06 = loadamberparams GLYCAM_06j.dat Loading parameters: /opt/software/amber/16/dat/leap/parm/GLYCAM_06j.dat Reading title: GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011 >> ## >> # >> # load all prep files for polysaccharides >> # >> loadamberprep GLYCAM_06j-1.prep Loading Prep file: /opt/software/amber/16/dat/leap/prep/GLYCAM_06j-1.prep Loaded UNIT: 0AA Loaded UNIT: 0AB Loaded UNIT: 0AD Loaded UNIT: 0AE Loaded UNIT: 0AF Loaded UNIT: 0AU Loaded UNIT: 0BA Loaded UNIT: 0BB Loaded UNIT: 0BC Loaded UNIT: 0BD Loaded UNIT: 0BU Loaded UNIT: 0CA Loaded UNIT: 0CB Loaded UNIT: 0CD Loaded UNIT: 0CU Loaded UNIT: 0DA Loaded UNIT: 0DB Loaded UNIT: 0DD Loaded UNIT: 0DU Loaded UNIT: 0EA Loaded UNIT: 0EB Loaded UNIT: 0FA Loaded UNIT: 0FB Loaded UNIT: 0GA Loaded UNIT: 0GB Loaded UNIT: 0GL Loaded UNIT: 0HA Loaded UNIT: 0HB Loaded UNIT: 0JA Loaded UNIT: 0JB Loaded UNIT: 0JD Loaded UNIT: 0JU Loaded UNIT: 0KA Loaded UNIT: 0KB Loaded UNIT: 0LA Loaded UNIT: 0LB Loaded UNIT: 0MA Loaded UNIT: 0MB Loaded UNIT: 0NA Loaded UNIT: 0NB Loaded UNIT: 0OA Loaded UNIT: 0OB Loaded UNIT: 0PA Loaded UNIT: 0PB Loaded UNIT: 0PD Loaded UNIT: 0PU Loaded UNIT: 0QA Loaded UNIT: 0QB Loaded UNIT: 0RA Loaded UNIT: 0RB Loaded UNIT: 0RD Loaded UNIT: 0RU Loaded UNIT: 0SA Loaded UNIT: 0SB Loaded UNIT: 0TA Loaded UNIT: 0TB Loaded UNIT: 0TV Loaded UNIT: 0Tv Loaded UNIT: 0UA Loaded UNIT: 0UB Loaded UNIT: 0VA Loaded UNIT: 0VB 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TRB Loaded UNIT: TTA Loaded UNIT: TTB Loaded UNIT: TUA Loaded UNIT: TUB Loaded UNIT: TXA Loaded UNIT: TXB Loaded UNIT: TZA Loaded UNIT: TZB Loaded UNIT: TaA Loaded UNIT: TaB Loaded UNIT: TdA Loaded UNIT: TdB Loaded UNIT: TeA Loaded UNIT: TeB Loaded UNIT: TfA Loaded UNIT: TfB Loaded UNIT: TgA Loaded UNIT: TgB Loaded UNIT: ThA Loaded UNIT: ThB Loaded UNIT: TkA Loaded UNIT: TkB Loaded UNIT: TlA Loaded UNIT: TlB Loaded UNIT: TmA Loaded UNIT: TmB Loaded UNIT: TnA Loaded UNIT: TnB Loaded UNIT: ToA Loaded UNIT: ToB Loaded UNIT: TqA Loaded UNIT: TqB Loaded UNIT: TrA Loaded UNIT: TrB Loaded UNIT: TtA Loaded UNIT: TtB Loaded UNIT: TuA Loaded UNIT: TuB Loaded UNIT: TxA Loaded UNIT: TxB Loaded UNIT: TzA Loaded UNIT: TzB Loaded UNIT: UBD Loaded UNIT: UBU Loaded UNIT: UCD Loaded UNIT: UCU Loaded UNIT: UEA Loaded UNIT: UEB Loaded UNIT: UGA Loaded UNIT: UGB Loaded UNIT: UJD Loaded UNIT: UJU Loaded UNIT: UKA Loaded UNIT: UKB Loaded UNIT: ULA Loaded UNIT: ULB Loaded UNIT: UMA Loaded UNIT: UMB Loaded UNIT: UNA Loaded UNIT: UNB Loaded UNIT: UPD Loaded UNIT: UPU Loaded UNIT: UTA Loaded UNIT: UTB Loaded UNIT: UVA Loaded UNIT: UVB Loaded UNIT: UWA Loaded UNIT: UWB Loaded UNIT: UYA Loaded UNIT: UYB Loaded UNIT: UbD Loaded UNIT: UbU Loaded UNIT: UcD Loaded UNIT: UcU Loaded UNIT: UeA Loaded UNIT: UeB Loaded UNIT: UgA Loaded UNIT: UgB Loaded UNIT: UjD Loaded UNIT: UjU Loaded UNIT: UkA Loaded UNIT: UkB Loaded UNIT: UlA Loaded UNIT: UlB Loaded UNIT: UmA Loaded UNIT: UmB Loaded UNIT: UnA Loaded UNIT: UnB Loaded UNIT: UpD Loaded UNIT: UpU Loaded UNIT: UtA Loaded UNIT: UtB Loaded UNIT: UvA Loaded UNIT: UvB Loaded UNIT: UwA Loaded UNIT: UwB Loaded UNIT: UyA Loaded UNIT: UyB Loaded UNIT: VBD Loaded UNIT: VBU Loaded UNIT: VCD Loaded UNIT: VCU Loaded UNIT: VEA Loaded UNIT: VEB Loaded UNIT: VGA Loaded UNIT: VGB Loaded UNIT: VJD Loaded UNIT: VJU Loaded UNIT: VKA Loaded UNIT: VKB Loaded UNIT: VLA Loaded UNIT: VLB Loaded UNIT: VMA Loaded UNIT: VMB Loaded UNIT: VNA Loaded UNIT: VNB Loaded UNIT: VPD Loaded UNIT: VPU Loaded UNIT: VTA Loaded UNIT: VTB Loaded UNIT: VVA Loaded UNIT: VVB Loaded UNIT: VWA Loaded UNIT: VWB Loaded UNIT: VYA Loaded UNIT: VYB Loaded UNIT: VbD Loaded UNIT: VbU Loaded UNIT: VcD Loaded UNIT: VcU Loaded UNIT: VeA Loaded UNIT: VeB Loaded UNIT: VgA Loaded UNIT: VgB Loaded UNIT: VjD Loaded UNIT: VjU Loaded UNIT: VkA Loaded UNIT: VkB Loaded UNIT: VlA Loaded UNIT: VlB Loaded UNIT: VmA Loaded UNIT: VmB Loaded UNIT: VnA Loaded UNIT: VnB Loaded UNIT: VpD Loaded UNIT: VpU Loaded UNIT: VtA Loaded UNIT: VtB Loaded UNIT: VvA Loaded UNIT: VvB Loaded UNIT: VwA Loaded UNIT: VwB Loaded UNIT: VyA Loaded UNIT: VyB Loaded UNIT: WAA Loaded UNIT: WAB Loaded UNIT: WBA Loaded UNIT: WBB Loaded UNIT: WBD Loaded UNIT: WBU Loaded UNIT: WCA Loaded UNIT: WCB Loaded UNIT: WCD Loaded UNIT: WCU Loaded UNIT: WDA Loaded UNIT: WDB Loaded UNIT: WEA Loaded UNIT: WEB Loaded UNIT: WFA Loaded UNIT: WFB Loaded UNIT: WGA Loaded UNIT: WGB Loaded UNIT: WHA Loaded UNIT: WHB Loaded UNIT: WJA Loaded UNIT: WJB Loaded UNIT: WJD Loaded UNIT: WJU Loaded UNIT: WKA Loaded UNIT: WKB Loaded UNIT: WLA Loaded UNIT: WLB Loaded UNIT: WMA Loaded UNIT: WMB Loaded UNIT: WNA Loaded UNIT: WNB Loaded UNIT: WOA Loaded UNIT: WOB Loaded UNIT: WPA Loaded UNIT: WPB Loaded UNIT: WPD Loaded UNIT: WPU Loaded UNIT: WQA Loaded UNIT: WQB Loaded UNIT: WRA Loaded UNIT: WRB Loaded UNIT: WTA Loaded UNIT: WTB Loaded UNIT: WUA Loaded UNIT: WUB Loaded UNIT: WVA Loaded UNIT: WVB Loaded UNIT: WWA Loaded UNIT: WWB Loaded UNIT: WXA Loaded UNIT: WXB Loaded UNIT: WYA Loaded UNIT: WYB Loaded UNIT: WZA Loaded UNIT: WZB Loaded UNIT: WaA Loaded UNIT: WaB Loaded UNIT: WbA Loaded UNIT: WbB Loaded UNIT: WbD Loaded UNIT: WbU Loaded UNIT: WcA Loaded UNIT: WcB Loaded UNIT: WcD Loaded UNIT: WcU Loaded UNIT: WdA Loaded UNIT: WdB Loaded UNIT: WdR Loaded UNIT: WeA Loaded UNIT: WeB Loaded UNIT: WfA Loaded UNIT: WfB Loaded UNIT: WgA Loaded UNIT: WgB Loaded UNIT: WhA Loaded UNIT: WhB Loaded UNIT: WjA Loaded UNIT: WjB Loaded UNIT: WjD Loaded UNIT: WjU Loaded UNIT: WkA Loaded UNIT: WkB Loaded UNIT: WlA Loaded UNIT: WlB Loaded UNIT: WmA Loaded UNIT: WmB Loaded UNIT: WnA Loaded UNIT: WnB Loaded UNIT: WoA Loaded UNIT: WoB Loaded UNIT: WpA Loaded UNIT: WpB Loaded UNIT: WpD Loaded UNIT: WpU Loaded UNIT: WqA Loaded UNIT: WqB Loaded UNIT: WrA Loaded UNIT: WrB Loaded UNIT: WtA Loaded UNIT: WtB Loaded UNIT: WuA Loaded UNIT: WuB Loaded UNIT: WvA Loaded UNIT: WvB Loaded UNIT: WwA Loaded UNIT: WwB Loaded UNIT: WxA Loaded UNIT: WxB Loaded UNIT: WyA Loaded UNIT: WyB Loaded UNIT: WzA Loaded UNIT: WzB Loaded UNIT: XEA Loaded UNIT: XEB Loaded UNIT: XGA Loaded UNIT: XGB Loaded UNIT: XKA Loaded UNIT: XKB Loaded UNIT: XLA Loaded UNIT: XLB Loaded UNIT: XMA Loaded UNIT: XMB Loaded UNIT: XNA Loaded UNIT: XNB Loaded UNIT: XTA Loaded UNIT: XTB Loaded UNIT: XeA Loaded UNIT: XeB Loaded UNIT: XgA Loaded UNIT: XgB Loaded UNIT: XkA Loaded UNIT: XkB Loaded UNIT: XlA Loaded UNIT: XlB Loaded UNIT: XmA Loaded UNIT: XmB Loaded UNIT: XnA Loaded UNIT: XnB Loaded UNIT: XtA Loaded UNIT: XtB Loaded UNIT: YAA Loaded UNIT: YAB Loaded UNIT: YAF Loaded UNIT: YDA Loaded UNIT: YDB Loaded UNIT: YEA Loaded UNIT: YEB Loaded UNIT: YFA Loaded UNIT: YFB Loaded UNIT: YGA Loaded UNIT: YGB Loaded UNIT: YGa Loaded UNIT: YHA Loaded UNIT: YHB Loaded UNIT: YKA Loaded UNIT: YKB Loaded UNIT: YLA Loaded UNIT: YLB Loaded UNIT: YMA Loaded UNIT: YMB Loaded UNIT: YNA Loaded UNIT: YNB Loaded UNIT: YOA Loaded UNIT: YOB Loaded UNIT: YQA Loaded UNIT: YQB Loaded UNIT: YRA Loaded UNIT: YRB Loaded UNIT: YTA Loaded UNIT: YTB Loaded UNIT: YTV Loaded UNIT: YTv Loaded UNIT: YUA Loaded UNIT: YUB Loaded UNIT: YXA Loaded UNIT: YXB Loaded UNIT: YZA Loaded UNIT: YZB Loaded UNIT: YaA Loaded UNIT: YaB Loaded UNIT: YdA Loaded UNIT: YdB Loaded UNIT: YeA Loaded UNIT: YeB Loaded UNIT: YfA Loaded UNIT: YfB Loaded UNIT: YgA Loaded UNIT: YgB Loaded UNIT: YhA Loaded UNIT: YhB Loaded UNIT: YkA Loaded UNIT: YkB Loaded UNIT: YlA Loaded UNIT: YlB Loaded UNIT: YmA Loaded UNIT: YmB Loaded UNIT: YnA Loaded UNIT: YnB Loaded UNIT: YoA Loaded UNIT: YoB Loaded UNIT: YqA Loaded UNIT: YqB Loaded UNIT: YrA Loaded UNIT: YrB Loaded UNIT: YtA Loaded UNIT: YtB Loaded UNIT: YtV Loaded UNIT: Ytv Loaded UNIT: YuA Loaded UNIT: YuB Loaded UNIT: YxA Loaded UNIT: YxB Loaded UNIT: YzA Loaded UNIT: YzB Loaded UNIT: ZAA Loaded UNIT: ZAB Loaded UNIT: ZAD Loaded UNIT: ZAU Loaded UNIT: ZDA Loaded UNIT: ZDB Loaded UNIT: ZDD Loaded UNIT: ZDU Loaded UNIT: ZEA Loaded UNIT: ZEB Loaded UNIT: ZFA Loaded UNIT: ZFB Loaded UNIT: ZGA Loaded UNIT: ZGB Loaded UNIT: ZHA Loaded UNIT: ZHB Loaded UNIT: ZKA Loaded UNIT: ZKB Loaded UNIT: ZLA Loaded UNIT: ZLB Loaded UNIT: ZMA Loaded UNIT: ZMB Loaded UNIT: ZNA Loaded UNIT: ZNB Loaded UNIT: ZOA Loaded UNIT: ZOB Loaded UNIT: ZOLS Loaded UNIT: ZOLT Loaded UNIT: ZQA Loaded UNIT: ZQB Loaded UNIT: ZRA Loaded UNIT: ZRB Loaded UNIT: ZRD Loaded UNIT: ZRU Loaded UNIT: ZTA Loaded UNIT: ZTB Loaded UNIT: ZUA Loaded UNIT: ZUB Loaded UNIT: ZXA Loaded UNIT: ZXB Loaded UNIT: ZXD Loaded UNIT: ZXU Loaded UNIT: ZZA Loaded UNIT: ZZB Loaded UNIT: ZaA Loaded UNIT: ZaB Loaded UNIT: ZaD Loaded UNIT: ZaU Loaded UNIT: ZdA Loaded UNIT: ZdB Loaded UNIT: ZdD Loaded UNIT: ZdU Loaded UNIT: ZeA Loaded UNIT: ZeB Loaded UNIT: ZfA Loaded UNIT: ZfB Loaded UNIT: ZgA Loaded UNIT: ZgB Loaded UNIT: ZhA Loaded UNIT: ZhB Loaded UNIT: ZkA Loaded UNIT: ZkB Loaded UNIT: ZlA Loaded UNIT: ZlB Loaded UNIT: ZmA Loaded UNIT: ZmB Loaded UNIT: ZnA Loaded UNIT: ZnB Loaded UNIT: ZoA Loaded UNIT: ZoB Loaded UNIT: ZqA Loaded UNIT: ZqB Loaded UNIT: ZrA Loaded UNIT: ZrB Loaded UNIT: ZrD Loaded UNIT: ZrU Loaded UNIT: ZtA Loaded UNIT: ZtB Loaded UNIT: ZuA Loaded UNIT: ZuB Loaded UNIT: ZxA Loaded UNIT: ZxB Loaded UNIT: ZxD Loaded UNIT: ZxU Loaded UNIT: ZzA Loaded UNIT: ZzB >> # >> # load lib files >> # >> # for attaching glycans to proteins >> loadOff GLYCAM_amino_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_amino_06j_12SB.lib Loading: HYP Loading: NLN Loading: OLP Loading: OLS Loading: OLT >> loadOff GLYCAM_aminoct_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib Loading: CHYP Loading: CNLN Loading: COLP Loading: COLS Loading: COLT >> loadOff GLYCAM_aminont_06j_12SB.lib Loading library: /opt/software/amber/16/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib Loading: NHYP Loading: NNLN Loading: NOLP Loading: NOLS Loading: NOLT >> ## add residue maps for linking glycans to proteins >> ## Note! use of these requires sourcing the ff12SB leaprc and loading the amino >> ## libraries commented out in the load libs section >> addPdbResMap { >> { 0 "OLS" "NOLS" } { 1 "OLS" "COLS" } >> { 0 "OLT" "NOLT" } { 1 "OLT" "COLT" } >> { 0 "OLP" "NOLP" } { 1 "OLP" "COLP" } >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "NLN" "NNLN" } { 1 "NLN" "CNLN" } >> } Substituting map 0HYP -> NHYP for 0HYP -> HYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP >> # >> # for explicit solvent and ions >> # >> # the following assumes most users want to use tip3p as the >> # explicit solvent model >> # this can easily switched by the following commands in leap: >> # WAT = TP5 >> # loadamberparams frcmod.tip5p >> # >> loadOff solvents.lib # solvents Loading library: /opt/software/amber/16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 # set default water model >> WAT = TP3 >> loadOff atomic_ions.lib # load ions library Loading library: /opt/software/amber/16/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 >> # to use ions for TIP5P, you will need to use a different frcmod below >> # If desired, see the AMBER manual for additional ion force field options. >> ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P Loading parameters: /opt/software/amber/16/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > g1dr9 = loadPdb "1dr9_tleap.pdb" Loading PDB file: ./1dr9_tleap.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue VAL, term: Terminal/beginning, seq. number: 0 to: NVAL. (Residue 1: ILE, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: VAL, Nonterminal, was not found in name map.) (Residue 4: THR, Nonterminal, was not found in name map.) (Residue 5: LYS, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: VAL, Nonterminal, was not found in name map.) (Residue 8: LYS, Nonterminal, was not found in name map.) (Residue 9: GLU, Nonterminal, was not found in name map.) (Residue 10: VAL, Nonterminal, was not found in name map.) (Residue 11: ALA, Nonterminal, was not found in name map.) (Residue 12: THR, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: SER, Nonterminal, was not found in name map.) (Residue 15: CYX, Nonterminal, was not found in name map.) (Residue 16: GLY, Nonterminal, was not found in name map.) (Residue 17: HIE, Nonterminal, was not found in name map.) (Residue 18: NLN, Nonterminal, was not found in name map.) (Residue 19: VAL, Nonterminal, was not found in name map.) (Residue 20: SER, Nonterminal, was not found in name map.) (Residue 21: VAL, Nonterminal, was not found in name map.) (Residue 22: GLU, Nonterminal, was not found in name map.) (Residue 23: GLU, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: ALA, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: THR, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ILE, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: TRP, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: LYS, Nonterminal, was not found in name map.) (Residue 34: GLU, Nonterminal, was not found in name map.) (Residue 35: LYS, Nonterminal, was not found in name map.) (Residue 36: LYS, Nonterminal, was not found in name map.) (Residue 37: MET, Nonterminal, was not found in name map.) (Residue 38: VAL, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: THR, Nonterminal, was not found in name map.) (Residue 41: MET, Nonterminal, was not found in name map.) (Residue 42: MET, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLY, Nonterminal, was not found in name map.) (Residue 45: ASP, Nonterminal, was not found in name map.) (Residue 46: MET, Nonterminal, was not found in name map.) (Residue 47: ASN, Nonterminal, was not found in name map.) (Residue 48: ILE, Nonterminal, was not found in name map.) (Residue 49: TRP, Nonterminal, was not found in name map.) (Residue 50: PRO, Nonterminal, was not found in name map.) (Residue 51: GLU, Nonterminal, was not found in name map.) (Residue 52: TYR, Nonterminal, was not found in name map.) (Residue 53: LYS, Nonterminal, was not found in name map.) (Residue 54: NLN, Nonterminal, was not found in name map.) (Residue 55: ARG, Nonterminal, was not found in name map.) (Residue 56: THR, Nonterminal, was not found in name map.) (Residue 57: ILE, Nonterminal, was not found in name map.) (Residue 58: PHE, Nonterminal, was not found in name map.) (Residue 59: ASP, Nonterminal, was not found in name map.) (Residue 60: ILE, Nonterminal, was not found in name map.) (Residue 61: THR, Nonterminal, was not found in name map.) (Residue 62: ASN, Nonterminal, was not found in name map.) (Residue 63: NLN, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: ILE, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: ILE, Nonterminal, was not found in name map.) (Residue 69: LEU, Nonterminal, was not found in name map.) (Residue 70: ALA, Nonterminal, was not found in name map.) (Residue 71: LEU, Nonterminal, was not found in name map.) (Residue 72: ARG, Nonterminal, was not found in name map.) (Residue 73: PRO, Nonterminal, was not found in name map.) (Residue 74: SER, Nonterminal, was not found in name map.) (Residue 75: ASP, Nonterminal, was not found in name map.) (Residue 76: GLU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: THR, Nonterminal, was not found in name map.) (Residue 79: TYR, Nonterminal, was not found in name map.) (Residue 80: GLU, Nonterminal, was not found in name map.) (Residue 81: CYX, Nonterminal, was not found in name map.) (Residue 82: VAL, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: LEU, Nonterminal, was not found in name map.) (Residue 85: LYS, Nonterminal, was not found in name map.) (Residue 86: TYR, Nonterminal, was not found in name map.) (Residue 87: GLU, Nonterminal, was not found in name map.) (Residue 88: LYS, Nonterminal, was not found in name map.) (Residue 89: ASP, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: PHE, Nonterminal, was not found in name map.) (Residue 92: LYS, Nonterminal, was not found in name map.) (Residue 93: ARG, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: HIE, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: ALA, Nonterminal, was not found in name map.) (Residue 98: GLU, Nonterminal, was not found in name map.) (Residue 99: VAL, Nonterminal, was not found in name map.) (Residue 100: THR, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: SER, Nonterminal, was not found in name map.) (Residue 103: VAL, Nonterminal, was not found in name map.) (Residue 104: LYS, Nonterminal, was not found in name map.) (Residue 105: ALA, Nonterminal, was not found in name map.) (Residue 106: ASP, Nonterminal, was not found in name map.) (Residue 107: PHE, Nonterminal, was not found in name map.) (Residue 108: PRO, Nonterminal, was not found in name map.) (Residue 109: THR, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: ILE, Nonterminal, was not found in name map.) (Residue 113: SER, Nonterminal, was not found in name map.) (Residue 114: ASP, Nonterminal, was not found in name map.) (Residue 115: PHE, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: ILE, Nonterminal, was not found in name map.) (Residue 118: PRO, Nonterminal, was not found in name map.) (Residue 119: THR, Nonterminal, was not found in name map.) (Residue 120: SER, Nonterminal, was not found in name map.) (Residue 121: ASN, Nonterminal, was not found in name map.) (Residue 122: ILE, Nonterminal, was not found in name map.) (Residue 123: ARG, Nonterminal, was not found in name map.) (Residue 124: ARG, Nonterminal, was not found in name map.) (Residue 125: ILE, Nonterminal, was not found in name map.) (Residue 126: ILE, Nonterminal, was not found in name map.) (Residue 127: CYX, Nonterminal, was not found in name map.) (Residue 128: SER, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: SER, Nonterminal, was not found in name map.) (Residue 131: GLY, Nonterminal, was not found in name map.) (Residue 132: GLY, Nonterminal, was not found in name map.) (Residue 133: PHE, Nonterminal, was not found in name map.) (Residue 134: PRO, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: PRO, Nonterminal, was not found in name map.) (Residue 137: HIS, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: SER, Nonterminal, was not found in name map.) (Residue 140: TRP, Nonterminal, was not found in name map.) (Residue 141: LEU, Nonterminal, was not found in name map.) (Residue 142: GLU, Nonterminal, was not found in name map.) (Residue 143: ASN, Nonterminal, was not found in name map.) (Residue 144: GLY, Nonterminal, was not found in name map.) (Residue 145: GLU, Nonterminal, was not found in name map.) (Residue 146: GLU, Nonterminal, was not found in name map.) (Residue 147: LEU, Nonterminal, was not found in name map.) (Residue 148: ASN, Nonterminal, was not found in name map.) (Residue 149: ALA, Nonterminal, was not found in name map.) (Residue 150: ILE, Nonterminal, was not found in name map.) (Residue 151: NLN, Nonterminal, was not found in name map.) (Residue 152: THR, Nonterminal, was not found in name map.) (Residue 153: THR, Nonterminal, was not found in name map.) (Residue 154: VAL, Nonterminal, was not found in name map.) (Residue 155: SER, Nonterminal, was not found in name map.) (Residue 156: GLN, Nonterminal, was not found in name map.) (Residue 157: ASP, Nonterminal, was not found in name map.) (Residue 158: PRO, Nonterminal, was not found in name map.) (Residue 159: GLU, Nonterminal, was not found in name map.) (Residue 160: THR, Nonterminal, was not found in name map.) (Residue 161: GLU, Nonterminal, was not found in name map.) (Residue 162: LEU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ALA, Nonterminal, was not found in name map.) (Residue 165: VAL, Nonterminal, was not found in name map.) (Residue 166: SER, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LYS, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ASP, Nonterminal, was not found in name map.) (Residue 171: PHE, Nonterminal, was not found in name map.) (Residue 172: NLN, Nonterminal, was not found in name map.) (Residue 173: MET, Nonterminal, was not found in name map.) (Residue 174: THR, Nonterminal, was not found in name map.) (Residue 175: THR, Nonterminal, was not found in name map.) (Residue 176: NLN, Nonterminal, was not found in name map.) (Residue 177: HIP, Nonterminal, was not found in name map.) (Residue 178: SER, Nonterminal, was not found in name map.) (Residue 179: PHE, Nonterminal, was not found in name map.) (Residue 180: MET, Nonterminal, was not found in name map.) (Residue 181: CYX, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: ILE, Nonterminal, was not found in name map.) (Residue 184: LYS, Nonterminal, was not found in name map.) (Residue 185: TYR, Nonterminal, was not found in name map.) (Residue 186: GLY, Nonterminal, was not found in name map.) (Residue 187: HIS, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ARG, Nonterminal, was not found in name map.) (Residue 190: VAL, Nonterminal, was not found in name map.) (Residue 191: NLN, Nonterminal, was not found in name map.) (Residue 192: GLN, Nonterminal, was not found in name map.) (Residue 193: THR, Nonterminal, was not found in name map.) (Residue 194: PHE, Nonterminal, was not found in name map.) (Residue 195: ASN, Nonterminal, was not found in name map.) (Residue 196: TRP, Nonterminal, was not found in name map.) (Residue 197: NLN, Nonterminal, was not found in name map.) (Residue 198: THR, Nonterminal, was not found in name map.) Mapped residue ALA, term: Terminal/last, seq. number: 199 to: CALA. (Residue 200: 0YB, Terminal/last, was not found in name map.) (Residue 201: 0YB, Terminal/last, was not found in name map.) (Residue 202: 0YB, Terminal/last, was not found in name map.) (Residue 203: 0YB, Terminal/last, was not found in name map.) (Residue 204: 0YB, Terminal/last, was not found in name map.) (Residue 205: 0YB, Terminal/last, was not found in name map.) (Residue 206: 0YB, Terminal/last, was not found in name map.) (Residue 207: 0YB, Terminal/last, was not found in name map.) Joining NVAL - ILE Joining ILE - HIE Joining HIE - VAL Joining VAL - THR Joining THR - LYS Joining LYS - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - THR Joining THR - LEU Joining LEU - SER Joining SER - CYX Joining CYX - GLY Joining GLY - HIE Joining HIE - NLN Joining NLN - VAL Joining VAL - SER Joining SER - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - THR Joining THR - ARG Joining ARG - ILE Joining ILE - TYR Joining TYR - TRP Joining TRP - GLN Joining GLN - LYS Joining LYS - GLU Joining GLU - LYS Joining LYS - LYS Joining LYS - MET Joining MET - VAL Joining VAL - LEU Joining LEU - THR Joining THR - MET Joining MET - MET Joining MET - SER Joining SER - GLY Joining GLY - ASP Joining ASP - MET Joining MET - ASN Joining ASN - ILE Joining ILE - TRP Joining TRP - PRO Joining PRO - GLU Joining GLU - TYR Joining TYR - LYS Joining LYS - NLN Joining NLN - ARG Joining ARG - THR Joining THR - ILE Joining ILE - PHE Joining PHE - ASP Joining ASP - ILE Joining ILE - THR Joining THR - ASN Joining ASN - NLN Joining NLN - LEU Joining LEU - SER Joining SER - ILE Joining ILE - VAL Joining VAL - ILE Joining ILE - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - PRO Joining PRO - SER Joining SER - ASP Joining ASP - GLU Joining GLU - GLY Joining GLY - THR Joining THR - TYR Joining TYR - GLU Joining GLU - CYX Joining CYX - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - GLU Joining GLU - LYS Joining LYS - ASP Joining ASP - ALA Joining ALA - PHE Joining PHE - LYS Joining LYS - ARG Joining ARG - GLU Joining GLU - HIE Joining HIE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - THR Joining THR - LEU Joining LEU - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - PRO Joining PRO - THR Joining THR - PRO Joining PRO - SER Joining SER - ILE Joining ILE - SER Joining SER - ASP Joining ASP - PHE Joining PHE - GLU Joining GLU - ILE Joining ILE - PRO Joining PRO - THR Joining THR - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ARG Joining ARG - ARG Joining ARG - ILE Joining ILE - ILE Joining ILE - CYX Joining CYX - SER Joining SER - THR Joining THR - SER Joining SER - GLY Joining GLY - GLY Joining GLY - PHE Joining PHE - PRO Joining PRO - GLU Joining GLU - PRO Joining PRO - HIE Joining HIE - LEU Joining LEU - SER Joining SER - TRP Joining TRP - LEU Joining LEU - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - ILE Joining ILE - NLN Joining NLN - THR Joining THR - THR Joining THR - VAL Joining VAL - SER Joining SER - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - GLU Joining GLU - THR Joining THR - GLU Joining GLU - LEU Joining LEU - TYR Joining TYR - ALA Joining ALA - VAL Joining VAL - SER Joining SER - SER Joining SER - LYS Joining LYS - LEU Joining LEU - ASP Joining ASP - PHE Joining PHE - NLN Joining NLN - MET Joining MET - THR Joining THR - THR Joining THR - NLN Joining NLN - HIP Joining HIP - SER Joining SER - PHE Joining PHE - MET Joining MET - CYX Joining CYX - LEU Joining LEU - ILE Joining ILE - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - HIE Joining HIE - LEU Joining LEU - ARG Joining ARG - VAL Joining VAL - NLN Joining NLN - GLN Joining GLN - THR Joining THR - PHE Joining PHE - ASN Joining ASN - TRP Joining TRP - NLN Joining NLN - THR Joining THR - CALA total atoms in file: 1716 Leap added 1681 missing atoms according to residue templates: 1681 H / lone pairs > bond g1dr9.16.SG g1dr9.82.SG > bond g1dr9.128.SG g1dr9.182.SG > solvateOct g1dr9 TIP3PBOX 14.0 Scaling up box by a factor of 1.092462 to meet diagonal cut criterion Solute vdw bounding box: 33.962 40.129 98.387 Total bounding box for atom centers: 128.976 128.976 128.976 (box expansion for 'iso' is 264.4%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 7 y= 7 z= 7 Adding box at: x=0 y=0 z=0 Center of solvent box is: 56.323047, 56.323047, 56.323047 Adding box at: x=0 y=0 z=1 Center of solvent box is: 56.323047, 56.323047, 37.548698 Adding box at: x=0 y=0 z=2 Center of solvent box is: 56.323047, 56.323047, 18.774349 Adding box at: x=0 y=0 z=3 Center of solvent box is: 56.323047, 56.323047, 0.000000 Adding box at: x=0 y=0 z=4 Center of solvent box is: 56.323047, 56.323047, -18.774349 Adding box at: x=0 y=0 z=5 Center of solvent box is: 56.323047, 56.323047, -37.548698 Adding box at: x=0 y=0 z=6 Center of solvent box is: 56.323047, 56.323047, -56.323047 Adding box at: x=0 y=1 z=0 Center of solvent box is: 56.323047, 37.548698, 56.323047 Adding box at: x=0 y=1 z=1 Center of solvent box is: 56.323047, 37.548698, 37.548698 Adding box at: x=0 y=1 z=2 Center of solvent box is: 56.323047, 37.548698, 18.774349 Adding box at: x=0 y=1 z=3 Center of solvent box is: 56.323047, 37.548698, 0.000000 Adding box at: x=0 y=1 z=4 Center of solvent box is: 56.323047, 37.548698, -18.774349 Adding box at: x=0 y=1 z=5 Center of solvent box is: 56.323047, 37.548698, -37.548698 Adding box at: x=0 y=1 z=6 Center of solvent box is: 56.323047, 37.548698, -56.323047 Adding box at: x=0 y=2 z=0 Center of solvent box is: 56.323047, 18.774349, 56.323047 Adding box at: x=0 y=2 z=1 Center of solvent box is: 56.323047, 18.774349, 37.548698 Adding box at: x=0 y=2 z=2 Center of solvent box is: 56.323047, 18.774349, 18.774349 Adding box at: x=0 y=2 z=3 Center of solvent box is: 56.323047, 18.774349, 0.000000 Adding box at: x=0 y=2 z=4 Center of solvent box is: 56.323047, 18.774349, -18.774349 Adding box at: x=0 y=2 z=5 Center of solvent box is: 56.323047, 18.774349, -37.548698 Adding box at: x=0 y=2 z=6 Center of solvent box is: 56.323047, 18.774349, -56.323047 Adding box at: x=0 y=3 z=0 Center of solvent box is: 56.323047, 0.000000, 56.323047 Adding box at: x=0 y=3 z=1 Center of solvent box is: 56.323047, 0.000000, 37.548698 Adding box at: x=0 y=3 z=2 Center of solvent box is: 56.323047, 0.000000, 18.774349 Adding box at: x=0 y=3 z=3 Center of solvent box is: 56.323047, 0.000000, 0.000000 Adding box at: x=0 y=3 z=4 Center of solvent box is: 56.323047, 0.000000, -18.774349 Adding box at: x=0 y=3 z=5 Center of solvent box is: 56.323047, 0.000000, -37.548698 Adding box at: x=0 y=3 z=6 Center of solvent box is: 56.323047, 0.000000, -56.323047 Adding box at: x=0 y=4 z=0 Center of solvent box is: 56.323047, -18.774349, 56.323047 Adding box at: x=0 y=4 z=1 Center of solvent box is: 56.323047, -18.774349, 37.548698 Adding box at: x=0 y=4 z=2 Center of solvent box is: 56.323047, -18.774349, 18.774349 Adding box at: x=0 y=4 z=3 Center of solvent box is: 56.323047, -18.774349, 0.000000 Adding box at: x=0 y=4 z=4 Center of solvent box is: 56.323047, -18.774349, -18.774349 Adding box at: x=0 y=4 z=5 Center of solvent box is: 56.323047, -18.774349, -37.548698 Adding box at: x=0 y=4 z=6 Center of solvent box is: 56.323047, -18.774349, -56.323047 Adding box at: x=0 y=5 z=0 Center of solvent box is: 56.323047, -37.548698, 56.323047 Adding box at: x=0 y=5 z=1 Center of solvent box is: 56.323047, -37.548698, 37.548698 Adding box at: x=0 y=5 z=2 Center of solvent box is: 56.323047, -37.548698, 18.774349 Adding box at: x=0 y=5 z=3 Center of solvent box is: 56.323047, -37.548698, 0.000000 Adding box at: x=0 y=5 z=4 Center of solvent box is: 56.323047, -37.548698, -18.774349 Adding box at: x=0 y=5 z=5 Center of solvent box is: 56.323047, -37.548698, -37.548698 Adding box at: x=0 y=5 z=6 Center of solvent box is: 56.323047, -37.548698, -56.323047 Adding box at: x=0 y=6 z=0 Center of solvent box is: 56.323047, -56.323047, 56.323047 Adding box at: x=0 y=6 z=1 Center of solvent box is: 56.323047, -56.323047, 37.548698 Adding box at: x=0 y=6 z=2 Center of solvent box is: 56.323047, -56.323047, 18.774349 Adding box at: x=0 y=6 z=3 Center of solvent box is: 56.323047, -56.323047, 0.000000 Adding box at: x=0 y=6 z=4 Center of solvent box is: 56.323047, -56.323047, -18.774349 Adding box at: x=0 y=6 z=5 Center of solvent box is: 56.323047, -56.323047, -37.548698 Adding box at: x=0 y=6 z=6 Center of solvent box is: 56.323047, -56.323047, -56.323047 Adding box at: x=1 y=0 z=0 Center of solvent box is: 37.548698, 56.323047, 56.323047 Adding box at: x=1 y=0 z=1 Center of solvent box is: 37.548698, 56.323047, 37.548698 Adding box at: x=1 y=0 z=2 Center of solvent box is: 37.548698, 56.323047, 18.774349 Adding box at: x=1 y=0 z=3 Center of solvent box is: 37.548698, 56.323047, 0.000000 Adding box at: x=1 y=0 z=4 Center of solvent box is: 37.548698, 56.323047, -18.774349 Adding box at: x=1 y=0 z=5 Center of solvent box is: 37.548698, 56.323047, -37.548698 Adding box at: x=1 y=0 z=6 Center of solvent box is: 37.548698, 56.323047, -56.323047 Adding box at: x=1 y=1 z=0 Center of solvent box is: 37.548698, 37.548698, 56.323047 Adding box at: x=1 y=1 z=1 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=1 y=1 z=2 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=1 y=1 z=3 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=1 y=1 z=4 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=1 y=1 z=5 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=1 y=1 z=6 Center of solvent box is: 37.548698, 37.548698, -56.323047 Adding box at: x=1 y=2 z=0 Center of solvent box is: 37.548698, 18.774349, 56.323047 Adding box at: x=1 y=2 z=1 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=1 y=2 z=2 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=1 y=2 z=3 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=1 y=2 z=4 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=1 y=2 z=5 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=1 y=2 z=6 Center of solvent box is: 37.548698, 18.774349, -56.323047 Adding box at: x=1 y=3 z=0 Center of solvent box is: 37.548698, 0.000000, 56.323047 Adding box at: x=1 y=3 z=1 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=1 y=3 z=2 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=1 y=3 z=3 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=1 y=3 z=4 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=1 y=3 z=5 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=1 y=3 z=6 Center of solvent box is: 37.548698, 0.000000, -56.323047 Adding box at: x=1 y=4 z=0 Center of solvent box is: 37.548698, -18.774349, 56.323047 Adding box at: x=1 y=4 z=1 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=1 y=4 z=2 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=1 y=4 z=3 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=1 y=4 z=4 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=1 y=4 z=5 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=1 y=4 z=6 Center of solvent box is: 37.548698, -18.774349, -56.323047 Adding box at: x=1 y=5 z=0 Center of solvent box is: 37.548698, -37.548698, 56.323047 Adding box at: x=1 y=5 z=1 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=1 y=5 z=2 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=1 y=5 z=3 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=1 y=5 z=4 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=1 y=5 z=5 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=5 z=6 Center of solvent box is: 37.548698, -37.548698, -56.323047 Adding box at: x=1 y=6 z=0 Center of solvent box is: 37.548698, -56.323047, 56.323047 Adding box at: x=1 y=6 z=1 Center of solvent box is: 37.548698, -56.323047, 37.548698 Adding box at: x=1 y=6 z=2 Center of solvent box is: 37.548698, -56.323047, 18.774349 Adding box at: x=1 y=6 z=3 Center of solvent box is: 37.548698, -56.323047, 0.000000 Adding box at: x=1 y=6 z=4 Center of solvent box is: 37.548698, -56.323047, -18.774349 Adding box at: x=1 y=6 z=5 Center of solvent box is: 37.548698, -56.323047, -37.548698 Adding box at: x=1 y=6 z=6 Center of solvent box is: 37.548698, -56.323047, -56.323047 Adding box at: x=2 y=0 z=0 Center of solvent box is: 18.774349, 56.323047, 56.323047 Adding box at: x=2 y=0 z=1 Center of solvent box is: 18.774349, 56.323047, 37.548698 Adding box at: x=2 y=0 z=2 Center of solvent box is: 18.774349, 56.323047, 18.774349 Adding box at: x=2 y=0 z=3 Center of solvent box is: 18.774349, 56.323047, 0.000000 Adding box at: x=2 y=0 z=4 Center of solvent box is: 18.774349, 56.323047, -18.774349 Adding box at: x=2 y=0 z=5 Center of solvent box is: 18.774349, 56.323047, -37.548698 Adding box at: x=2 y=0 z=6 Center of solvent box is: 18.774349, 56.323047, -56.323047 Adding box at: x=2 y=1 z=0 Center of solvent box is: 18.774349, 37.548698, 56.323047 Adding box at: x=2 y=1 z=1 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=2 y=1 z=2 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=2 y=1 z=3 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=2 y=1 z=4 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=2 y=1 z=5 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=2 y=1 z=6 Center of solvent box is: 18.774349, 37.548698, -56.323047 Adding box at: x=2 y=2 z=0 Center of solvent box is: 18.774349, 18.774349, 56.323047 Adding box at: x=2 y=2 z=1 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=2 y=2 z=2 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=2 y=2 z=3 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=2 y=2 z=4 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=2 y=2 z=5 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=2 y=2 z=6 Center of solvent box is: 18.774349, 18.774349, -56.323047 Adding box at: x=2 y=3 z=0 Center of solvent box is: 18.774349, 0.000000, 56.323047 Adding box at: x=2 y=3 z=1 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=2 y=3 z=2 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=2 y=3 z=3 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=2 y=3 z=4 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=2 y=3 z=5 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=2 y=3 z=6 Center of solvent box is: 18.774349, 0.000000, -56.323047 Adding box at: x=2 y=4 z=0 Center of solvent box is: 18.774349, -18.774349, 56.323047 Adding box at: x=2 y=4 z=1 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=2 y=4 z=2 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=2 y=4 z=3 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=2 y=4 z=4 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=2 y=4 z=5 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=2 y=4 z=6 Center of solvent box is: 18.774349, -18.774349, -56.323047 Adding box at: x=2 y=5 z=0 Center of solvent box is: 18.774349, -37.548698, 56.323047 Adding box at: x=2 y=5 z=1 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=2 y=5 z=2 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=2 y=5 z=3 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=2 y=5 z=4 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=2 y=5 z=5 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=5 z=6 Center of solvent box is: 18.774349, -37.548698, -56.323047 Adding box at: x=2 y=6 z=0 Center of solvent box is: 18.774349, -56.323047, 56.323047 Adding box at: x=2 y=6 z=1 Center of solvent box is: 18.774349, -56.323047, 37.548698 Adding box at: x=2 y=6 z=2 Center of solvent box is: 18.774349, -56.323047, 18.774349 Adding box at: x=2 y=6 z=3 Center of solvent box is: 18.774349, -56.323047, 0.000000 Adding box at: x=2 y=6 z=4 Center of solvent box is: 18.774349, -56.323047, -18.774349 Adding box at: x=2 y=6 z=5 Center of solvent box is: 18.774349, -56.323047, -37.548698 Adding box at: x=2 y=6 z=6 Center of solvent box is: 18.774349, -56.323047, -56.323047 Adding box at: x=3 y=0 z=0 Center of solvent box is: 0.000000, 56.323047, 56.323047 Adding box at: x=3 y=0 z=1 Center of solvent box is: 0.000000, 56.323047, 37.548698 Adding box at: x=3 y=0 z=2 Center of solvent box is: 0.000000, 56.323047, 18.774349 Adding box at: x=3 y=0 z=3 Center of solvent box is: 0.000000, 56.323047, 0.000000 Adding box at: x=3 y=0 z=4 Center of solvent box is: 0.000000, 56.323047, -18.774349 Adding box at: x=3 y=0 z=5 Center of solvent box is: 0.000000, 56.323047, -37.548698 Adding box at: x=3 y=0 z=6 Center of solvent box is: 0.000000, 56.323047, -56.323047 Adding box at: x=3 y=1 z=0 Center of solvent box is: 0.000000, 37.548698, 56.323047 Adding box at: x=3 y=1 z=1 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=3 y=1 z=2 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=3 y=1 z=3 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=3 y=1 z=4 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=3 y=1 z=5 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=3 y=1 z=6 Center of solvent box is: 0.000000, 37.548698, -56.323047 Adding box at: x=3 y=2 z=0 Center of solvent box is: 0.000000, 18.774349, 56.323047 Adding box at: x=3 y=2 z=1 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=3 y=2 z=2 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=3 y=2 z=3 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=3 y=2 z=4 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=3 y=2 z=5 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=3 y=2 z=6 Center of solvent box is: 0.000000, 18.774349, -56.323047 Adding box at: x=3 y=3 z=0 Center of solvent box is: 0.000000, 0.000000, 56.323047 Adding box at: x=3 y=3 z=1 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=3 y=3 z=2 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=3 y=3 z=3 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=3 y=3 z=4 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=3 y=3 z=5 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=3 y=3 z=6 Center of solvent box is: 0.000000, 0.000000, -56.323047 Adding box at: x=3 y=4 z=0 Center of solvent box is: 0.000000, -18.774349, 56.323047 Adding box at: x=3 y=4 z=1 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=3 y=4 z=2 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=3 y=4 z=3 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=3 y=4 z=4 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=3 y=4 z=5 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=3 y=4 z=6 Center of solvent box is: 0.000000, -18.774349, -56.323047 Adding box at: x=3 y=5 z=0 Center of solvent box is: 0.000000, -37.548698, 56.323047 Adding box at: x=3 y=5 z=1 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=3 y=5 z=2 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=3 y=5 z=3 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=3 y=5 z=4 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=3 y=5 z=5 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=5 z=6 Center of solvent box is: 0.000000, -37.548698, -56.323047 Adding box at: x=3 y=6 z=0 Center of solvent box is: 0.000000, -56.323047, 56.323047 Adding box at: x=3 y=6 z=1 Center of solvent box is: 0.000000, -56.323047, 37.548698 Adding box at: x=3 y=6 z=2 Center of solvent box is: 0.000000, -56.323047, 18.774349 Adding box at: x=3 y=6 z=3 Center of solvent box is: 0.000000, -56.323047, 0.000000 Adding box at: x=3 y=6 z=4 Center of solvent box is: 0.000000, -56.323047, -18.774349 Adding box at: x=3 y=6 z=5 Center of solvent box is: 0.000000, -56.323047, -37.548698 Adding box at: x=3 y=6 z=6 Center of solvent box is: 0.000000, -56.323047, -56.323047 Adding box at: x=4 y=0 z=0 Center of solvent box is: -18.774349, 56.323047, 56.323047 Adding box at: x=4 y=0 z=1 Center of solvent box is: -18.774349, 56.323047, 37.548698 Adding box at: x=4 y=0 z=2 Center of solvent box is: -18.774349, 56.323047, 18.774349 Adding box at: x=4 y=0 z=3 Center of solvent box is: -18.774349, 56.323047, 0.000000 Adding box at: x=4 y=0 z=4 Center of solvent box is: -18.774349, 56.323047, -18.774349 Adding box at: x=4 y=0 z=5 Center of solvent box is: -18.774349, 56.323047, -37.548698 Adding box at: x=4 y=0 z=6 Center of solvent box is: -18.774349, 56.323047, -56.323047 Adding box at: x=4 y=1 z=0 Center of solvent box is: -18.774349, 37.548698, 56.323047 Adding box at: x=4 y=1 z=1 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=4 y=1 z=2 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=4 y=1 z=3 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=4 y=1 z=4 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=4 y=1 z=5 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=4 y=1 z=6 Center of solvent box is: -18.774349, 37.548698, -56.323047 Adding box at: x=4 y=2 z=0 Center of solvent box is: -18.774349, 18.774349, 56.323047 Adding box at: x=4 y=2 z=1 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=4 y=2 z=2 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=4 y=2 z=3 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=4 y=2 z=4 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=4 y=2 z=5 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=4 y=2 z=6 Center of solvent box is: -18.774349, 18.774349, -56.323047 Adding box at: x=4 y=3 z=0 Center of solvent box is: -18.774349, 0.000000, 56.323047 Adding box at: x=4 y=3 z=1 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=4 y=3 z=2 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=4 y=3 z=3 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=4 y=3 z=4 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=4 y=3 z=5 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=4 y=3 z=6 Center of solvent box is: -18.774349, 0.000000, -56.323047 Adding box at: x=4 y=4 z=0 Center of solvent box is: -18.774349, -18.774349, 56.323047 Adding box at: x=4 y=4 z=1 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=4 y=4 z=2 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=4 y=4 z=3 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=4 y=4 z=4 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=4 y=4 z=5 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=4 y=4 z=6 Center of solvent box is: -18.774349, -18.774349, -56.323047 Adding box at: x=4 y=5 z=0 Center of solvent box is: -18.774349, -37.548698, 56.323047 Adding box at: x=4 y=5 z=1 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=4 y=5 z=2 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=4 y=5 z=3 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=4 y=5 z=4 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=4 y=5 z=5 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=5 z=6 Center of solvent box is: -18.774349, -37.548698, -56.323047 Adding box at: x=4 y=6 z=0 Center of solvent box is: -18.774349, -56.323047, 56.323047 Adding box at: x=4 y=6 z=1 Center of solvent box is: -18.774349, -56.323047, 37.548698 Adding box at: x=4 y=6 z=2 Center of solvent box is: -18.774349, -56.323047, 18.774349 Adding box at: x=4 y=6 z=3 Center of solvent box is: -18.774349, -56.323047, 0.000000 Adding box at: x=4 y=6 z=4 Center of solvent box is: -18.774349, -56.323047, -18.774349 Adding box at: x=4 y=6 z=5 Center of solvent box is: -18.774349, -56.323047, -37.548698 Adding box at: x=4 y=6 z=6 Center of solvent box is: -18.774349, -56.323047, -56.323047 Adding box at: x=5 y=0 z=0 Center of solvent box is: -37.548698, 56.323047, 56.323047 Adding box at: x=5 y=0 z=1 Center of solvent box is: -37.548698, 56.323047, 37.548698 Adding box at: x=5 y=0 z=2 Center of solvent box is: -37.548698, 56.323047, 18.774349 Adding box at: x=5 y=0 z=3 Center of solvent box is: -37.548698, 56.323047, 0.000000 Adding box at: x=5 y=0 z=4 Center of solvent box is: -37.548698, 56.323047, -18.774349 Adding box at: x=5 y=0 z=5 Center of solvent box is: -37.548698, 56.323047, -37.548698 Adding box at: x=5 y=0 z=6 Center of solvent box is: -37.548698, 56.323047, -56.323047 Adding box at: x=5 y=1 z=0 Center of solvent box is: -37.548698, 37.548698, 56.323047 Adding box at: x=5 y=1 z=1 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=5 y=1 z=2 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=5 y=1 z=3 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=5 y=1 z=4 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=5 y=1 z=5 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=5 y=1 z=6 Center of solvent box is: -37.548698, 37.548698, -56.323047 Adding box at: x=5 y=2 z=0 Center of solvent box is: -37.548698, 18.774349, 56.323047 Adding box at: x=5 y=2 z=1 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=5 y=2 z=2 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=5 y=2 z=3 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=5 y=2 z=4 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=5 y=2 z=5 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=5 y=2 z=6 Center of solvent box is: -37.548698, 18.774349, -56.323047 Adding box at: x=5 y=3 z=0 Center of solvent box is: -37.548698, 0.000000, 56.323047 Adding box at: x=5 y=3 z=1 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=5 y=3 z=2 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=5 y=3 z=3 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=5 y=3 z=4 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=5 y=3 z=5 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=5 y=3 z=6 Center of solvent box is: -37.548698, 0.000000, -56.323047 Adding box at: x=5 y=4 z=0 Center of solvent box is: -37.548698, -18.774349, 56.323047 Adding box at: x=5 y=4 z=1 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=5 y=4 z=2 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=5 y=4 z=3 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=5 y=4 z=4 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=5 y=4 z=5 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=5 y=4 z=6 Center of solvent box is: -37.548698, -18.774349, -56.323047 Adding box at: x=5 y=5 z=0 Center of solvent box is: -37.548698, -37.548698, 56.323047 Adding box at: x=5 y=5 z=1 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=5 y=5 z=2 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=5 y=5 z=3 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=5 y=5 z=4 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=5 y=5 z=5 Center of solvent box is: -37.548698, -37.548698, -37.548698 Adding box at: x=5 y=5 z=6 Center of solvent box is: -37.548698, -37.548698, -56.323047 Adding box at: x=5 y=6 z=0 Center of solvent box is: -37.548698, -56.323047, 56.323047 Adding box at: x=5 y=6 z=1 Center of solvent box is: -37.548698, -56.323047, 37.548698 Adding box at: x=5 y=6 z=2 Center of solvent box is: -37.548698, -56.323047, 18.774349 Adding box at: x=5 y=6 z=3 Center of solvent box is: -37.548698, -56.323047, 0.000000 Adding box at: x=5 y=6 z=4 Center of solvent box is: -37.548698, -56.323047, -18.774349 Adding box at: x=5 y=6 z=5 Center of solvent box is: -37.548698, -56.323047, -37.548698 Adding box at: x=5 y=6 z=6 Center of solvent box is: -37.548698, -56.323047, -56.323047 Adding box at: x=6 y=0 z=0 Center of solvent box is: -56.323047, 56.323047, 56.323047 Adding box at: x=6 y=0 z=1 Center of solvent box is: -56.323047, 56.323047, 37.548698 Adding box at: x=6 y=0 z=2 Center of solvent box is: -56.323047, 56.323047, 18.774349 Adding box at: x=6 y=0 z=3 Center of solvent box is: -56.323047, 56.323047, 0.000000 Adding box at: x=6 y=0 z=4 Center of solvent box is: -56.323047, 56.323047, -18.774349 Adding box at: x=6 y=0 z=5 Center of solvent box is: -56.323047, 56.323047, -37.548698 Adding box at: x=6 y=0 z=6 Center of solvent box is: -56.323047, 56.323047, -56.323047 Adding box at: x=6 y=1 z=0 Center of solvent box is: -56.323047, 37.548698, 56.323047 Adding box at: x=6 y=1 z=1 Center of solvent box is: -56.323047, 37.548698, 37.548698 Adding box at: x=6 y=1 z=2 Center of solvent box is: -56.323047, 37.548698, 18.774349 Adding box at: x=6 y=1 z=3 Center of solvent box is: -56.323047, 37.548698, 0.000000 Adding box at: x=6 y=1 z=4 Center of solvent box is: -56.323047, 37.548698, -18.774349 Adding box at: x=6 y=1 z=5 Center of solvent box is: -56.323047, 37.548698, -37.548698 Adding box at: x=6 y=1 z=6 Center of solvent box is: -56.323047, 37.548698, -56.323047 Adding box at: x=6 y=2 z=0 Center of solvent box is: -56.323047, 18.774349, 56.323047 Adding box at: x=6 y=2 z=1 Center of solvent box is: -56.323047, 18.774349, 37.548698 Adding box at: x=6 y=2 z=2 Center of solvent box is: -56.323047, 18.774349, 18.774349 Adding box at: x=6 y=2 z=3 Center of solvent box is: -56.323047, 18.774349, 0.000000 Adding box at: x=6 y=2 z=4 Center of solvent box is: -56.323047, 18.774349, -18.774349 Adding box at: x=6 y=2 z=5 Center of solvent box is: -56.323047, 18.774349, -37.548698 Adding box at: x=6 y=2 z=6 Center of solvent box is: -56.323047, 18.774349, -56.323047 Adding box at: x=6 y=3 z=0 Center of solvent box is: -56.323047, 0.000000, 56.323047 Adding box at: x=6 y=3 z=1 Center of solvent box is: -56.323047, 0.000000, 37.548698 Adding box at: x=6 y=3 z=2 Center of solvent box is: -56.323047, 0.000000, 18.774349 Adding box at: x=6 y=3 z=3 Center of solvent box is: -56.323047, 0.000000, 0.000000 Adding box at: x=6 y=3 z=4 Center of solvent box is: -56.323047, 0.000000, -18.774349 Adding box at: x=6 y=3 z=5 Center of solvent box is: -56.323047, 0.000000, -37.548698 Adding box at: x=6 y=3 z=6 Center of solvent box is: -56.323047, 0.000000, -56.323047 Adding box at: x=6 y=4 z=0 Center of solvent box is: -56.323047, -18.774349, 56.323047 Adding box at: x=6 y=4 z=1 Center of solvent box is: -56.323047, -18.774349, 37.548698 Adding box at: x=6 y=4 z=2 Center of solvent box is: -56.323047, -18.774349, 18.774349 Adding box at: x=6 y=4 z=3 Center of solvent box is: -56.323047, -18.774349, 0.000000 Adding box at: x=6 y=4 z=4 Center of solvent box is: -56.323047, -18.774349, -18.774349 Adding box at: x=6 y=4 z=5 Center of solvent box is: -56.323047, -18.774349, -37.548698 Adding box at: x=6 y=4 z=6 Center of solvent box is: -56.323047, -18.774349, -56.323047 Adding box at: x=6 y=5 z=0 Center of solvent box is: -56.323047, -37.548698, 56.323047 Adding box at: x=6 y=5 z=1 Center of solvent box is: -56.323047, -37.548698, 37.548698 Adding box at: x=6 y=5 z=2 Center of solvent box is: -56.323047, -37.548698, 18.774349 Adding box at: x=6 y=5 z=3 Center of solvent box is: -56.323047, -37.548698, 0.000000 Adding box at: x=6 y=5 z=4 Center of solvent box is: -56.323047, -37.548698, -18.774349 Adding box at: x=6 y=5 z=5 Center of solvent box is: -56.323047, -37.548698, -37.548698 Adding box at: x=6 y=5 z=6 Center of solvent box is: -56.323047, -37.548698, -56.323047 Adding box at: x=6 y=6 z=0 Center of solvent box is: -56.323047, -56.323047, 56.323047 Adding box at: x=6 y=6 z=1 Center of solvent box is: -56.323047, -56.323047, 37.548698 Adding box at: x=6 y=6 z=2 Center of solvent box is: -56.323047, -56.323047, 18.774349 Adding box at: x=6 y=6 z=3 Center of solvent box is: -56.323047, -56.323047, 0.000000 Adding box at: x=6 y=6 z=4 Center of solvent box is: -56.323047, -56.323047, -18.774349 Adding box at: x=6 y=6 z=5 Center of solvent box is: -56.323047, -56.323047, -37.548698 Adding box at: x=6 y=6 z=6 Center of solvent box is: -56.323047, -56.323047, -56.323047 Volume: 1097885.722 A^3 (oct) Total mass 610659.206 amu, Density 0.924 g/cc Added 32538 residues. > #addIons g1dr9 Na+ 20 Cl- 24 > savepdb g1dr9 g1dr9_tleap.pdb Writing pdb file: g1dr9_tleap.pdb printing CRYST1 record to PDB file with box info Converting N-terminal residue name to PDB format: NVAL -> VAL Converting C-terminal residue name to PDB format: CALA -> ALA > saveAmberParm g1dr9 solvated_g1dr9.top solvated_g1dr9.crd Checking Unit. WARNING: There is a bond of 3.361144 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.502353 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: H1 H2 N H3 ** Warning: No sp2 improper torsion term for H-H-N3-CX atoms are: H1 H2 N CA ** Warning: No sp2 improper torsion term for H-H-N3-CX atoms are: H1 H3 N CA ** Warning: No sp2 improper torsion term for H-H-N3-CX atoms are: H2 H3 N CA ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ2 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ1 NZ HZ3 ** Warning: No sp2 improper torsion term for C8-H-N3-H atoms are: CE HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for H-H-N3-H atoms are: HZ1 HZ2 NZ HZ3 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 634 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 CALA 1 NVAL 1 WAT 32538 ) (no restraints) > quit Quit