Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # ----- this file is updated 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: /home/crystal/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: /home/crystal/amber11/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /home/crystal/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: /home/crystal/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: /home/crystal/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: /home/crystal/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 > # > # Load water and ions > # > loadOff ions94.lib Loading library: /home/crystal/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: /home/crystal/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'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "O2*" "O2'" } > { "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" } > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > { "OP1" "O1P" } > { "OP2" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > 2hom=loadpdb "2HOM_1_addH.pdb" Loading PDB file: ./2HOM_1_addH.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5. Mapped residue C, term: Nonterminal, seq. number: 1 to: RC. Mapped residue G, term: Nonterminal, seq. number: 2 to: RG. Mapped residue A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue C, term: Nonterminal, seq. number: 4 to: RC. Mapped residue U, term: Nonterminal, seq. number: 5 to: RU. Mapped residue C, term: Nonterminal, seq. number: 6 to: RC. Mapped residue G, term: Nonterminal, seq. number: 7 to: RG. Mapped residue G, term: Nonterminal, seq. number: 8 to: RG. Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue G, term: Nonterminal, seq. number: 10 to: RG. Mapped residue U, term: Nonterminal, seq. number: 11 to: RU. Mapped residue G, term: Nonterminal, seq. number: 12 to: RG. Mapped residue C, term: Nonterminal, seq. number: 13 to: RC. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue C, term: Nonterminal, seq. number: 15 to: RC. Mapped residue U, term: Nonterminal, seq. number: 16 to: RU. Mapped residue G, term: Nonterminal, seq. number: 17 to: RG. Mapped residue C, term: Nonterminal, seq. number: 18 to: RC. Mapped residue G, term: Nonterminal, seq. number: 19 to: RG. Mapped residue U, term: Nonterminal, seq. number: 20 to: RU. Mapped residue G, term: Nonterminal, seq. number: 21 to: RG. Mapped residue A, term: Nonterminal, seq. number: 22 to: RA. Mapped residue A, term: Nonterminal, seq. number: 23 to: RA. Mapped residue G, term: Nonterminal, seq. number: 24 to: RG. Mapped residue G, term: Nonterminal, seq. number: 25 to: RG. Mapped residue C, term: Nonterminal, seq. number: 26 to: RC. Mapped residue U, term: Nonterminal, seq. number: 27 to: RU. Mapped residue G, term: Nonterminal, seq. number: 28 to: RG. Mapped residue A, term: Nonterminal, seq. number: 29 to: RA. Mapped residue G, term: Nonterminal, seq. number: 30 to: RG. Mapped residue A, term: Nonterminal, seq. number: 31 to: RA. Mapped residue A, term: Nonterminal, seq. number: 32 to: RA. Mapped residue A, term: Nonterminal, seq. number: 33 to: RA. Mapped residue U, term: Nonterminal, seq. number: 34 to: RU. Mapped residue A, term: Nonterminal, seq. number: 35 to: RA. Mapped residue C, term: Nonterminal, seq. number: 36 to: RC. Mapped residue C, term: Nonterminal, seq. number: 37 to: RC. Mapped residue C, term: Nonterminal, seq. number: 38 to: RC. Mapped residue G, term: Nonterminal, seq. number: 39 to: RG. Mapped residue U, term: Nonterminal, seq. number: 40 to: RU. Mapped residue A, term: Nonterminal, seq. number: 41 to: RA. Mapped residue U, term: Nonterminal, seq. number: 42 to: RU. Mapped residue C, term: Nonterminal, seq. number: 43 to: RC. Mapped residue A, term: Nonterminal, seq. number: 44 to: RA. Mapped residue C, term: Nonterminal, seq. number: 45 to: RC. Mapped residue C, term: Nonterminal, seq. number: 46 to: RC. Mapped residue U, term: Nonterminal, seq. number: 47 to: RU. Mapped residue G, term: Nonterminal, seq. number: 48 to: RG. Mapped residue A, term: Nonterminal, seq. number: 49 to: RA. Mapped residue U, term: Nonterminal, seq. number: 50 to: RU. Mapped residue C, term: Nonterminal, seq. number: 51 to: RC. Mapped residue U, term: Nonterminal, seq. number: 52 to: RU. Mapped residue G, term: Nonterminal, seq. number: 53 to: RG. Mapped residue G, term: Nonterminal, seq. number: 54 to: RG. Mapped residue A, term: Nonterminal, seq. number: 55 to: RA. Mapped residue U, term: Nonterminal, seq. number: 56 to: RU. Mapped residue A, term: Nonterminal, seq. number: 57 to: RA. Mapped residue A, term: Nonterminal, seq. number: 58 to: RA. Mapped residue U, term: Nonterminal, seq. number: 59 to: RU. Mapped residue G, term: Nonterminal, seq. number: 60 to: RG. Mapped residue C, term: Nonterminal, seq. number: 61 to: RC. Mapped residue C, term: Nonterminal, seq. number: 62 to: RC. Mapped residue A, term: Nonterminal, seq. number: 63 to: RA. Mapped residue G, term: Nonterminal, seq. number: 64 to: RG. Mapped residue C, term: Nonterminal, seq. number: 65 to: RC. Mapped residue G, term: Nonterminal, seq. number: 66 to: RG. Mapped residue U, term: Nonterminal, seq. number: 67 to: RU. Mapped residue A, term: Nonterminal, seq. number: 68 to: RA. Mapped residue G, term: Nonterminal, seq. number: 69 to: RG. Mapped residue G, term: Nonterminal, seq. number: 70 to: RG. Mapped residue G, term: Nonterminal, seq. number: 71 to: RG. Mapped residue A, term: Nonterminal, seq. number: 72 to: RA. Mapped residue A, term: Nonterminal, seq. number: 73 to: RA. Mapped residue G, term: Nonterminal, seq. number: 74 to: RG. Mapped residue U, term: Nonterminal, seq. number: 75 to: RU. Mapped residue C, term: Nonterminal, seq. number: 76 to: RC. Mapped residue G, term: Nonterminal, seq. number: 77 to: RG. Mapped residue C, term: Nonterminal, seq. number: 78 to: RC. Mapped residue A, term: Terminal/last, seq. number: 79 to: RA3. (Residue 80: MG, Terminal/beginning, was not found in name map.) Unknown residue: MG number: 80 type: Terminal/beginning ..relaxing end constraints to try for a dbase match -no luck (Residue 81: MG, Nonterminal, was not found in name map.) Unknown residue: MG number: 81 type: Nonterminal (Residue 82: TPS, Terminal/last, was not found in name map.) Unknown residue: TPS number: 82 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining RG5 - RC Joining RC - RG Joining RG - RA Joining RA - RC Joining RC - RU Joining RU - RC Joining RC - RG Joining RG - RG Joining RG - RG Joining RG - RG Joining RG - RU Joining RU - RG Joining RG - RC Joining RC - RC Joining RC - RC Joining RC - RU Joining RU - RG Joining RG - RC Joining RC - RG Joining RG - RU Joining RU - RG Joining RG - RA Joining RA - RA Joining RA - RG Joining RG - RG Joining RG - RC Joining RC - RU Joining RU - RG Joining RG - RA Joining RA - RG Joining RG - RA Joining RA - RA Joining RA - RA Joining RA - RU Created a new atom named: H1'' 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 Joining RU - RA Joining RA - RC Joining RC - RC Joining RC - RC Joining RC - RG Joining RG - RU Joining RU - RA Joining RA - RU Created a new atom named: H1'' 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 Joining RU - RC Created a new atom named: H1'' 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 Joining RC - RA Joining RA - RC Joining RC - RC Joining RC - RU Joining RU - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RU Joining RU - RG Joining RG - RG Joining RG - RA Joining RA - RU Joining RU - RA Joining RA - RA Joining RA - RU Joining RU - RG Joining RG - RC Joining RC - RC Joining RC - RA Joining RA - RG Joining RG - RC Joining RC - RG Joining RG - RU Created a new atom named: H1'' 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 Joining RU - RA Joining RA - RG Joining RG - RG Joining RG - RG Joining RG - RA Joining RA - RA Joining RA - RG Joining RG - RU Joining RU - RC Joining RC - RG Joining RG - RC Joining RC - RA3 Creating new UNIT for residue: MG sequence: 89 Created a new atom named: MG within residue: .R Creating new UNIT for residue: MG sequence: 90 Starting new chain with Created a new atom named: MG within residue: .R Creating new UNIT for residue: TPS sequence: 91 Starting new chain with Created a new atom named: CM2 within residue: .R Created a new atom named: N3 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: C5 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: CM4 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: C7 within residue: .R Created a new atom named: O7 within residue: .R Created a new atom named: N1A within residue: .R Created a new atom named: C2A within residue: .R Created a new atom named: N3A within residue: .R Created a new atom named: C4A within residue: .R Created a new atom named: N4A within residue: .R Created a new atom named: C5A within residue: .R Created a new atom named: C6A within residue: .R Created a new atom named: C7A within residue: .R Created a new atom named: P1 within residue: .R Created a new atom named: O1 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: O3 within residue: .R Created a new atom named: HM21 within residue: .R Created a new atom named: HM22 within residue: .R Created a new atom named: HM23 within residue: .R Created a new atom named: H2 within residue: .R Created a new atom named: HM41 within residue: .R Created a new atom named: HM42 within residue: .R Created a new atom named: HM43 within residue: .R Created a new atom named: H62 within residue: .R Created a new atom named: H63 within residue: .R Created a new atom named: H72 within residue: .R Created a new atom named: H73 within residue: .R Created a new atom named: H4A1 within residue: .R Created a new atom named: H4A2 within residue: .R Created a new atom named: H6A within residue: .R Created a new atom named: H7A2 within residue: .R Created a new atom named: H7A3 within residue: .R total atoms in file: 2578 Leap added 46 missing atoms according to residue templates: 32 Heavy 14 H / lone pairs The file contained 44 atoms not in residue templates > saveamberparm 2hom test.prmtop test.inpcrd Checking Unit. WARNING: There is a bond of 8.309758 angstroms between: ------- .R.A and .R.A

WARNING: The unperturbed charge of the unit: -79.000000 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. 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. Failed to generate parameters Parameter file was not saved. > desc 2hom.MG.1 ATOM Name: MG Type: Charge: 0.0000 Polarization: 0.0000 Element: Mg Atom flags: (decimal 131072 hex 0x20000) posfxd n posblt n posdrwn n selected n pert n notdisp n touched n posknwn Y internal n needsmin n needsbuild n Atom position: 31.301000, 36.964000, 68.260000 Atom velocity: 0.000000, 0.000000, 0.000000 NO BONDS > desc 2hom.MG RESIDUE name: MG RESIDUE sequence number: 89 RESIDUE PDB sequence number: 81 Type: undefined Connection atoms: Improper torsions: Contents: A > desc 2hom.42.32 ATOM Normal Perturbed Name: HO'2 HO'2 Type: HO HO Charge: 0.4186 0.000 Polarization: 0.0000 0.000 Element: H (not affected by pert) Atom flags: (decimal 131072 hex 0x20000) posfxd n posblt n posdrwn n selected n pert n notdisp n touched n posknwn Y internal n needsmin n needsbuild n Atom position: 8.349000, 41.137000, 56.708000 Atom velocity: 0.000000, 0.000000, 0.000000 Bonded to .R.A by a single bond.