log started: Wed Apr 21 12:30:45 2010 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # using parmbsc0 for nucleic acid. > # ----- 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" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /root/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /root/amber11/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > frcmodbsc0 = loadamberparams frcmod.parmbsc0 Loading parameters: /root/amber11/dat/leap/parm/frcmod.parmbsc0 Reading force field modification type file (frcmod) Reading title: modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/ > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /root/amber11/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /root/amber11/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /root/amber11/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /root/amber11/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > loadOff DNA_CI.lib Loading library: /root/amber11/dat/leap/lib/DNA_CI.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DC Loading: DC3 Loading: DC5 Loading: DG Loading: DG3 Loading: DG5 Loading: DT Loading: DT3 Loading: DT5 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /root/amber11/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /root/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } > { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } > { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } > { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } > { 0 "DG" "DG5" } { 1 "DG" "DG3" } > { 0 "DA" "DA5" } { 1 "DA" "DA3" } > { 0 "DC" "DC5" } { 1 "DC" "DC3" } > { 0 "DT" "DT5" } { 1 "DT" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "O2*" "O2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H2'" "H2'1" } > { "H2''" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > { "H5'" "H5'1" } > { "H5''" "H5'2" } > { "HO2'" "HO'2" } > { "HO5'" "H5T" } > { "HO3'" "H3T" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > { "OP1" "O1P" } > { "OP2" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > source leaprc.gaff ----- Source: /root/amber11/dat/leap/cmd/leaprc.gaff ----- Source of /root/amber11/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Wed Apr 21 12:30:56 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /root/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > > prp=loadamberprep prp.prepin Loading Prep file: ./prp.prepin Loaded UNIT: MOL > loadamberparams prp.frcmod Loading parameters: ./prp.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > complex=loadpdb 2hy9-complex.pdb Loading PDB file: ./2hy9-complex.pdb Enter zPdbReadScan from call depth 0. -- residue 27: duplicate [ C] atoms (total 44) -- residue 27: duplicate [ H] atoms (total 2) -- residue 27: duplicate [ N] atoms (total 8) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue DA, term: Terminal/beginning, seq. number: 0 to: DA5. (Residue 1: DA, Nonterminal, was not found in name map.) (Residue 2: DA, Nonterminal, was not found in name map.) (Residue 3: DG, Nonterminal, was not found in name map.) (Residue 4: DG, Nonterminal, was not found in name map.) (Residue 5: DG, Nonterminal, was not found in name map.) (Residue 6: DT, Nonterminal, was not found in name map.) (Residue 7: DT, Nonterminal, was not found in name map.) (Residue 8: DA, Nonterminal, was not found in name map.) (Residue 9: DG, Nonterminal, was not found in name map.) (Residue 10: DG, Nonterminal, was not found in name map.) (Residue 11: DG, Nonterminal, was not found in name map.) (Residue 12: DT, Nonterminal, was not found in name map.) (Residue 13: DT, Nonterminal, was not found in name map.) (Residue 14: DA, Nonterminal, was not found in name map.) (Residue 15: DG, Nonterminal, was not found in name map.) (Residue 16: DG, Nonterminal, was not found in name map.) (Residue 17: DG, Nonterminal, was not found in name map.) (Residue 18: DT, Nonterminal, was not found in name map.) (Residue 19: DT, Nonterminal, was not found in name map.) (Residue 20: DA, Nonterminal, was not found in name map.) (Residue 21: DG, Nonterminal, was not found in name map.) (Residue 22: DG, Nonterminal, was not found in name map.) (Residue 23: DG, Nonterminal, was not found in name map.) (Residue 24: DA, Nonterminal, was not found in name map.) Mapped residue DA, term: Terminal/last, seq. number: 25 to: DA3. (Residue 26: MOL, Terminal/last, was not found in name map.) Created a new atom named: 'HO5 within residue: .R Joining DA5 - DA Joining DA - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DA Joining DA - DA3 Created a new atom named: 'HO3 within residue: .R Created a new atom named: C within residue: .R Created a new atom named: N within residue: .R Created a new atom named: H within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 663 Leap added 326 missing atoms according to residue templates: 52 Heavy 274 H / lone pairs The file contained 5 atoms not in residue templates > complex=loadpdb 2hy9-complex.pdb Loading PDB file: ./2hy9-complex.pdb Enter zPdbReadScan from call depth 0. -- residue 27: duplicate [ C] atoms (total 44) -- residue 27: duplicate [ H] atoms (total 2) -- residue 27: duplicate [ N] atoms (total 8) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue DA, term: Terminal/beginning, seq. number: 0 to: DA5. (Residue 1: DA, Nonterminal, was not found in name map.) (Residue 2: DA, Nonterminal, was not found in name map.) (Residue 3: DG, Nonterminal, was not found in name map.) (Residue 4: DG, Nonterminal, was not found in name map.) (Residue 5: DG, Nonterminal, was not found in name map.) (Residue 6: DT, Nonterminal, was not found in name map.) (Residue 7: DT, Nonterminal, was not found in name map.) (Residue 8: DA, Nonterminal, was not found in name map.) (Residue 9: DG, Nonterminal, was not found in name map.) (Residue 10: DG, Nonterminal, was not found in name map.) (Residue 11: DG, Nonterminal, was not found in name map.) (Residue 12: DT, Nonterminal, was not found in name map.) (Residue 13: DT, Nonterminal, was not found in name map.) (Residue 14: DA, Nonterminal, was not found in name map.) (Residue 15: DG, Nonterminal, was not found in name map.) (Residue 16: DG, Nonterminal, was not found in name map.) (Residue 17: DG, Nonterminal, was not found in name map.) (Residue 18: DT, Nonterminal, was not found in name map.) (Residue 19: DT, Nonterminal, was not found in name map.) (Residue 20: DA, Nonterminal, was not found in name map.) (Residue 21: DG, Nonterminal, was not found in name map.) (Residue 22: DG, Nonterminal, was not found in name map.) (Residue 23: DG, Nonterminal, was not found in name map.) (Residue 24: DA, Nonterminal, was not found in name map.) Mapped residue DA, term: Terminal/last, seq. number: 25 to: DA3. (Residue 26: MOL, Terminal/last, was not found in name map.) Joining DA5 - DA Joining DA - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DT Joining DT - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DG - DA Joining DA - DA3 Created a new atom named: C within residue: .R Created a new atom named: N within residue: .R Created a new atom named: H within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 663 Leap added 324 missing atoms according to residue templates: 52 Heavy 272 H / lone pairs The file contained 3 atoms not in residue templates > saveamberparm complex 2hy9-complex.prmtop 2hy9-complex.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -20.999998 is not zero. 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. Failed to generate parameters Parameter file was not saved.