log started: Tue Jun 18 13:56:40 2019 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "op" "O" "sp3" } >> { "oq" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /cm/shared/apps/Amber-18/amber18/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /cm/shared/apps/Amber-18/amber18/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /cm/shared/apps/Amber-18/amber18/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Tue Jun 18 13:56:48 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: /cm/shared/apps/Amber-18/amber18/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/dat/leap/cmd/leaprc.water.tip3p ----- Source of /cm/shared/apps/Amber-18/amber18/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham 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" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /cm/shared/apps/Amber-18/amber18/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /cm/shared/apps/Amber-18/amber18/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: /cm/shared/apps/Amber-18/amber18/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) >> > > loadamberparams sfr.frcmod Loading parameters: ./sfr.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff sfr.frcmod sfr.lib Error: saveOff: Argument #1 is type String must be of type: [unit parameter_set list] usage: saveOff > sfr = loadmol2 sfr.mol2 Loading Mol2 file: ./sfr.mol2 Reading MOLECULE named UNK > chech sfr Error: Error from the parser: syntax error > check sfr Checking 'sfr'.... Warning: Close contact of 1.428384 angstroms between .R.A

and .R.A Checking parameters for unit 'sfr'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 1 Unit is OK. > loadamberparams sfr.frcmod Loading parameters: ./sfr.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff sfr sfr.lib Saving sfr. Building topology. Building atom parameters. > saveamberparm sfr sfr.prmtop sfr.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 8 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 UNK 1 ) (no restraints) > loadamberparams sfr.frcmod Loading parameters: ./sfr.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff sfr.lib Loading library: ./sfr.lib Loading: lig Loading: lig2 Loading: sfr > gol = loadmol2 gol.mol2 Loading Mol2 file: ./gol.mol2 Reading MOLECULE named GOL > check gol Checking 'gol'.... Checking parameters for unit 'gol'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > loadamberparams gol.frcmod Loading parameters: ./gol.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff gol gol.lib Saving gol. Building topology. Building atom parameters. > saveamberparm gol gol.prmtop gol.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 0 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 GOL 1 ) (no restraints) > loadamberparams gol.frcmod Loading parameters: ./gol.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff gol.lib Loading library: ./gol.lib Loading: gol Loading: lig Loading: lig2 > comp = loadpdb 5uj4_r.pdb Loading PDB file: ./5uj4_r.pdb Matching PDB residue names to LEaP variables. Mapped residue HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. Mapped residue VAL, term: Terminal/last, seq. number: 267 to: CVAL. Warning: Unknown residue: SFR number: 268 type: Terminal/beginning ..relaxing end constraints to try for a dbase match Warning: -no luck Warning: Unknown residue: GOL number: 269 type: Terminal/last ..relaxing end constraints to try for a dbase match Warning: -no luck Added missing heavy atom: .R.A Creating new UNIT for residue: SFR sequence: 269 Created a new atom named: O72 within residue: .R Created a new atom named: C7 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: N4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: S1 within residue: .R Created a new atom named: C31 within residue: .R Created a new atom named: O71 within residue: .R Created a new atom named: C61 within residue: .R Created a new atom named: O62 within residue: .R Created a new atom named: C62 within residue: .R Created a new atom named: C14 within residue: .R Created a new atom named: C15 within residue: .R Created a new atom named: C16 within residue: .R Created a new atom named: C17 within residue: .R Created a new atom named: O18 within residue: .R Created a new atom named: O32 within residue: .R Created a new atom named: O31 within residue: .R Created a new atom named: HO72 within residue: .R Created a new atom named: HO62 within residue: .R Created a new atom named: HO31 within residue: .R Created a new atom named: H62B within residue: .R Created a new atom named: H62A within residue: .R Created a new atom named: H17A within residue: .R Created a new atom named: H16A within residue: .R Created a new atom named: H15A within residue: .R Created a new atom named: HN4 within residue: .R Created a new atom named: H62 within residue: .R Created a new atom named: H61 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H5 within residue: .R Created a new atom named: H17 within residue: .R Created a new atom named: H16 within residue: .R Created a new atom named: H15 within residue: .R Created a new atom named: H14 within residue: .R Created a new atom named: H2 within residue: .R Creating new UNIT for residue: GOL sequence: 270 Starting new chain with Created a new atom named: C1 within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: O3 within residue: .R Created a new atom named: HO3 within residue: .R Created a new atom named: HO2 within residue: .R Created a new atom named: HO1 within residue: .R Created a new atom named: H32 within residue: .R Created a new atom named: H31 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: H12 within residue: .R Created a new atom named: H11 within residue: .R total atoms in file: 4047 Leap added 1 missing atom according to residue templates: 1 Heavy The file contained 52 atoms not in residue templates > solvatebox comp TIP3PBOX 12.0 (using default radius 1.500000 for O72) (using default radius 1.500000 for C7) (using default radius 1.500000 for C6) (using default radius 1.500000 for N4) (using default radius 1.500000 for C5) (using default radius 1.500000 for C3) (using default radius 1.500000 for C2) (using default radius 1.500000 for S1) (using default radius 1.500000 for C31) (using default radius 1.500000 for O71) (using default radius 1.500000 for C61) (using default radius 1.500000 for O62) (using default radius 1.500000 for C62) (using default radius 1.500000 for C14) (using default radius 1.500000 for C15) (using default radius 1.500000 for C16) (using default radius 1.500000 for C17) (using default radius 1.500000 for O18) (using default radius 1.500000 for O32) (using default radius 1.500000 for O31) (using default radius 1.500000 for HO72) (using default radius 1.500000 for HO62) (using default radius 1.500000 for HO31) (using default radius 1.500000 for C1) (using default radius 1.500000 for O1) (using default radius 1.500000 for C2) (using default radius 1.500000 for O2) (using default radius 1.500000 for C3) (using default radius 1.500000 for O3) Solute vdw bounding box: 65.479 42.634 50.886 Total bounding box for atom centers: 89.479 66.634 74.886 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 4 z= 4 (using default radius 1.500000 for O72) (using default radius 1.500000 for C7) (using default radius 1.500000 for C6) (using default radius 1.500000 for N4) (using default radius 1.500000 for C5) (using default radius 1.500000 for C3) (using default radius 1.500000 for C2) (using default radius 1.500000 for S1) (using default radius 1.500000 for C31) (using default radius 1.500000 for O71) (using default radius 1.500000 for C61) (using default radius 1.500000 for O62) (using default radius 1.500000 for C62) (using default radius 1.500000 for C14) (using default radius 1.500000 for C15) (using default radius 1.500000 for C16) (using default radius 1.500000 for C17) (using default radius 1.500000 for O18) (using default radius 1.500000 for O32) (using default radius 1.500000 for O31) (using default radius 1.500000 for HO72) (using default radius 1.500000 for HO62) (using default radius 1.500000 for HO31) (using default radius 1.500000 for C1) (using default radius 1.500000 for O1) (using default radius 1.500000 for C2) (using default radius 1.500000 for O2) (using default radius 1.500000 for C3) (using default radius 1.500000 for O3) Total vdw box size: 92.604 69.707 77.685 angstroms. Volume: 501466.956 A^3 Mass > 249896.110 amu, Density > 0.828 g/cc (type - hence mass - of one or more atoms could not be found) Added 12292 residues. > charge comp Total unperturbed charge: -1.000000 Total perturbed charge: -1.000000 > addions comp Na+ 0 1 Na+ ion required to neutralize. Adding 1 counter ions to "comp" using 1A grid Used default radius 1.50 for 52 atoms Total solute charge: -1.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.37 to 7.37 Box: enclosing: -38.71 -27.70 -31.15 39.19 27.31 31.97 sized: 89.29 100.30 96.85 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.50% of box, grid points 52398 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in comp at (-18.90, 9.74, 0.48). Done adding ions. > saveamberparm comp 5uj4.prmtop 5uj4.inpcrd Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A
does not have a type. FATAL: Atom .R.A
does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Error: Failed to generate parameters Warning: Parameter file was not saved. > quit Quit Exiting LEaP: Errors = 3; Warnings = 6; Notes = 0.