[rajjak@apollo2 2H7S]$ tleap
-I: Adding /usr/local/amber9/dat/leap/prep to search path.
-I: Adding /usr/local/amber9/dat/leap/lib to search path.
-I: Adding /usr/local/amber9/dat/leap/parm to search path.
-I: Adding /usr/local/amber9/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source tleapcommand
----- Source: ./tleapcommand
----- Source of ./tleapcommand done
----- Source: /usr/local/amber9/dat/leap/cmd/leaprc.ff99
----- Source of /usr/local/amber9/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /usr/local/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib
Loading parameters: ./parm99_mod.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: ./frcmod.heme_all
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme
Unknown keyword: N.B.: para in parameter file.
Unknown keyword:   six-coor in parameter file.
Unknown keyword: Force fiel in parameter file.
Unknown keyword:    Univers in parameter file.
Unknown keyword:            in parameter file.
Unknown keyword: I modified in parameter file.
Loading Prep file: ./heme_all.in
Loading PDB file: ./2H7S_mod.pdb
  total atoms in file: 3393
  Leap added 3373 missing atoms according to residue templates:
       3373 H / lone pairs
Checking 'mol'....
WARNING: There is a bond of 4.889570 angstroms between: 
-------  .R<HEM 357>.A<FE 9> and .R<HEM 357>.A<C 82>
WARNING: The unperturbed charge of the unit: -20.000000 is not zero.
Warning: Close contact of 2.246168 angstroms between .R<LEU 14>.A<HD13 13> and .R<LEU 14>.A<HA 4>
Warning: Close contact of 1.910426 angstroms between .R<ASN 33>.A<HD22 12> and .R<VAL 44>.A<HG12 9>
Warning: Close contact of 1.844847 angstroms between .R<GLN 39>.A<HE22 15> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.936478 angstroms between .R<GLN 39>.A<NE2 13> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.506529 angstroms between .R<GLU 40>.A<OE1 12> and .R<GLU 40>.A<H 2>
Warning: Close contact of 2.011145 angstroms between .R<GLU 40>.A<HG3 10> and .R<MET 336>.A<HE3 15>
Warning: Close contact of 2.195527 angstroms between .R<GLN 46>.A<O 17> and .R<ARG 67>.A<HH22 22>
Warning: Close contact of 1.867627 angstroms between .R<ARG 67>.A<HH21 21> and .R<WAT 419>.A<H1 1>
Warning: Close contact of 2.178894 angstroms between .R<ARG 72>.A<HH11 18> and .R<ARG 72>.A<HG3 10>
Warning: Close contact of 1.035785 angstroms between .R<ASP 77>.A<OD2 10> and .R<HID 80>.A<HD1 10>
Warning: Close contact of 2.219096 angstroms between .R<ASP 77>.A<HB2 6> and .R<WAT 465>.A<H2 2>
Warning: Close contact of 1.687677 angstroms between .R<PRO 86>.A<O 14> and .R<GLY 298>.A<H 2>
Warning: Close contact of 1.954963 angstroms between .R<ILE 88>.A<HD13 17> and .R<ILE 88>.A<H 2>
Warning: Close contact of 1.164720 angstroms between .R<TYR 96>.A<HH 15> and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.153334 angstroms between .R<TYR 96>.A<HH 15> and .R<THR 101>.A<OG1 11>
Warning: Close contact of 2.166421 angstroms between .R<TYR 96>.A<OH 14> and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.140836 angstroms between .R<GLN 108>.A<HE22 15> and .R<GLN 108>.A<HB3 7>
Warning: Close contact of 1.850847 angstroms between .R<GLN 110>.A<HE22 15> and .R<ASN 229>.A<HA 4>
Warning: Close contact of 1.823980 angstroms between .R<ARG 112>.A<HH11 18> and .R<HEM 357>.A<O1D 80>
Warning: Close contact of 1.339097 angstroms between .R<GLN 117>.A<HE21 14> and .R<WAT 433>.A<H1 1>
Warning: Close contact of 1.452897 angstroms between .R<ASP 125>.A<HA 4> and .R<WAT 496>.A<H2 2>
Warning: Close contact of 1.827194 angstroms between .R<ARG 130>.A<HD2 12> and .R<ARG 130>.A<HA 4>
Warning: Close contact of 1.762332 angstroms between .R<ILE 131>.A<HD13 17> and .R<ILE 162>.A<HD13 17>
Warning: Close contact of 1.785659 angstroms between .R<ALA 135>.A<HA 4> and .R<WAT 506>.A<H1 1>
Warning: Close contact of 1.668065 angstroms between .R<SER 141>.A<HB3 7> and .R<WAT 457>.A<H1 1>
Warning: Close contact of 1.648441 angstroms between .R<GLN 145>.A<H 2> and .R<WAT 448>.A<H2 2>
Warning: Close contact of 2.124973 angstroms between .R<GLY 146>.A<H 2> and .R<WAT 448>.A<O 3>
Warning: Close contact of 1.092559 angstroms between .R<GLY 146>.A<H 2> and .R<WAT 448>.A<H1 1>
Warning: Close contact of 1.790061 angstroms between .R<THR 151>.A<HG23 10> and .R<SER 258>.A<HG 9>
Warning: Close contact of 0.976382 angstroms between .R<THR 151>.A<HG21 8> and .R<THR 151>.A<H 2>
Warning: Close contact of 1.906989 angstroms between .R<LEU 165>.A<HB3 7> and .R<WAT 498>.A<H2 2>
Warning: Close contact of 0.839659 angstroms between .R<HID 176>.A<HD2 15> and .R<WAT 436>.A<H1 1>
Warning: Close contact of 2.184279 angstroms between .R<THR 181>.A<HG21 8> and .R<VAL 247>.A<HG23 14>
Warning: Close contact of 2.231917 angstroms between .R<ASP 182>.A<O 12> and .R<ARG 186>.A<H 2>
Warning: Close contact of 2.138727 angstroms between .R<MET 184>.A<HB3 7> and .R<PHE 193>.A<HE1 12>
Warning: Close contact of 1.731171 angstroms between .R<MET 191>.A<HE3 15> and .R<ALA 196>.A<HA 4>
Warning: Close contact of 1.620850 angstroms between .R<PHE 193>.A<HD2 18> and .R<WAT 487>.A<H1 1>
Warning: Close contact of 1.133502 angstroms between .R<ALA 194>.A<HA 4> and .R<WAT 487>.A<H2 2>
Warning: Close contact of 1.956045 angstroms between .R<GLU 209>.A<O 15> and .R<GLN 213>.A<HE22 15>
Warning: Close contact of 1.363557 angstroms between .R<ARG 211>.A<HH11 18> and .R<WAT 451>.A<H2 2>
Warning: Close contact of 2.188873 angstroms between .R<ARG 211>.A<HE 15> and .R<WAT 451>.A<H2 2>
Warning: Close contact of 2.117503 angstroms between .R<GLN 213>.A<HG3 10> and .R<GLN 213>.A<H 2>
Warning: Close contact of 2.164919 angstroms between .R<GLY 216>.A<H 2> and .R<SER 221>.A<HB3 7>
Warning: Close contact of 1.764190 angstroms between .R<ASP 218>.A<HA 4> and .R<WAT 517>.A<H2 2>
Warning: Close contact of 1.958026 angstroms between .R<ASN 229>.A<HD22 12> and .R<ASN 229>.A<HA 4>
Warning: Close contact of 2.120345 angstroms between .R<ILE 233>.A<HD11 15> and .R<GLU 237>.A<HB2 6>
Warning: Close contact of 1.722452 angstroms between .R<GLU 237>.A<O 15> and .R<MET 241>.A<H 2>
Warning: Close contact of 1.832649 angstroms between .R<GLU 237>.A<HG2 9> and .R<ARG 240>.A<HH21 21>
Warning: Close contact of 1.411345 angstroms between .R<VAL 247>.A<HG13 10> and .R<WAT 519>.A<O 3>
Warning: Close contact of 0.894151 angstroms between .R<VAL 247>.A<HG13 10> and .R<WAT 519>.A<H2 2>
Warning: Close contact of 2.083850 angstroms between .R<VAL 247>.A<HB 6> and .R<WAT 430>.A<H1 1>
Warning: Close contact of 1.873508 angstroms between .R<LEU 250>.A<HD23 17> and .R<WAT 428>.A<H1 1>
Warning: Close contact of 1.906005 angstroms between .R<ASP 251>.A<HA 4> and .R<WAT 472>.A<H2 2>
Warning: Close contact of 2.228194 angstroms between .R<VAL 254>.A<HB 6> and .R<WAT 472>.A<H1 1>
Warning: Close contact of 1.976005 angstroms between .R<ASN 255>.A<H 2> and .R<WAT 472>.A<O 3>
Warning: Close contact of 0.438342 angstroms between .R<ASN 255>.A<H 2> and .R<WAT 472>.A<H1 1>
Warning: Close contact of 2.120191 angstroms between .R<SER 267>.A<HA 4> and .R<PRO 268>.A<HD2 3>
Warning: Close contact of 1.968942 angstroms between .R<LEU 274>.A<HD23 17> and .R<ILE 281>.A<HD11 15>
Warning: Close contact of 0.246143 angstroms between .R<ARG 277>.A<HH21 21> and .R<ARG 280>.A<HH21 21>
Warning: Close contact of 2.248835 angstroms between .R<ARG 277>.A<HH21 21> and .R<ARG 280>.A<NH2 20>
Warning: Close contact of 1.353690 angstroms between .R<ARG 277>.A<NH2 20> and .R<ARG 280>.A<HH21 21>
Warning: Close contact of 0.711629 angstroms between .R<ALA 283>.A<H 2> and .R<WAT 513>.A<H2 2>
Warning: Close contact of 2.110204 angstroms between .R<ARG 290>.A<HH11 18> and .R<ARG 290>.A<HD2 12>
Warning: Close contact of 1.929369 angstroms between .R<LEU 294>.A<H 2> and .R<WAT 515>.A<H1 1>
Warning: Close contact of 0.654612 angstroms between .R<VAL 295>.A<H 2> and .R<WAT 515>.A<H2 2>
Warning: Close contact of 1.399941 angstroms between .R<GLY 298>.A<O 7> and .R<ARG 299>.A<HH11 18>
Warning: Close contact of 1.998699 angstroms between .R<GLY 298>.A<O 7> and .R<ARG 299>.A<HD3 13>
Warning: Close contact of 1.251292 angstroms between .R<ARG 299>.A<HE 15> and .R<WAT 474>.A<H2 2>
Warning: Close contact of 2.095108 angstroms between .R<LYS 313>.A<HE2 15> and .R<WAT 488>.A<H2 2>
Warning: Close contact of 1.964478 angstroms between .R<LYS 313>.A<HE2 15> and .R<WAT 504>.A<H1 1>
Warning: Close contact of 1.597401 angstroms between .R<GLN 322>.A<HE22 15> and .R<WAT 491>.A<H2 2>
Warning: Close contact of 2.212426 angstroms between .R<ARG 330>.A<HH21 21> and .R<WAT 452>.A<H2 2>
Warning: Close contact of 1.902618 angstroms between .R<ALA 334>.A<H 2> and .R<WAT 485>.A<H1 1>
Warning: Close contact of 2.201433 angstroms between .R<HEM 357>.A<HBM 61> and .R<HEM 357>.A<HV4 55>
Warning: Close contact of 2.241537 angstroms between .R<ARG 365>.A<HH22 22> and .R<WAT 526>.A<H2 2>
Warning: Close contact of 2.102031 angstroms between .R<ARG 365>.A<HH11 18> and .R<ARG 365>.A<HD2 12>
Warning: Close contact of 2.167108 angstroms between .R<GLU 373>.A<OE1 12> and .R<ARG 377>.A<HH12 19>
Warning: Close contact of 1.392790 angstroms between .R<GLU 373>.A<HG2 9> and .R<GLU 373>.A<H 2>
Warning: Close contact of 1.782277 angstroms between .R<ILE 389>.A<HD13 17> and .R<ILE 389>.A<H 2>
Warning: Close contact of 1.732702 angstroms between .R<WAT 426>.A<H1 1> and .R<WAT 436>.A<H2 2>
Warning: Close contact of 1.778697 angstroms between .R<WAT 429>.A<H2 2> and .R<WAT 517>.A<H1 1>
Checking parameters for unit 'mol'.
Checking for bond parameters.
Could not find bond parameter for: FE - C
Checking for angle parameters.
Could not find angle parameter: NO - FE - C
Could not find angle parameter: NP - FE - C
Could not find angle parameter: NO - FE - C
Could not find angle parameter: NP - FE - C
Could not find angle parameter: FE - C - O
Could not find angle parameter: FE - C - N
Could not find angle parameter: SH - FE - C
There are missing parameters.
check:  Warnings: 83
Unit is OK.
> deleteBond mol.357.9 mol.357.82
> check mol
Checking 'mol'....
WARNING: The unperturbed charge of the unit: -20.000000 is not zero.
Warning: Close contact of 2.246168 angstroms between .R<LEU 14>.A<HD13 13> and .R<LEU 14>.A<HA 4>
Warning: Close contact of 1.910426 angstroms between .R<ASN 33>.A<HD22 12> and .R<VAL 44>.A<HG12 9>
Warning: Close contact of 1.844847 angstroms between .R<GLN 39>.A<HE22 15> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.936478 angstroms between .R<GLN 39>.A<NE2 13> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.506529 angstroms between .R<GLU 40>.A<OE1 12> and .R<GLU 40>.A<H 2>
Warning: Close contact of 2.011145 angstroms between .R<GLU 40>.A<HG3 10> and .R<MET 336>.A<HE3 15>
Warning: Close contact of 2.195527 angstroms between .R<GLN 46>.A<O 17> and .R<ARG 67>.A<HH22 22>
Warning: Close contact of 1.867627 angstroms between .R<ARG 67>.A<HH21 21> and .R<WAT 419>.A<H1 1>
Warning: Close contact of 2.178894 angstroms between .R<ARG 72>.A<HH11 18> and .R<ARG 72>.A<HG3 10>
Warning: Close contact of 1.035785 angstroms between .R<ASP 77>.A<OD2 10> and .R<HID 80>.A<HD1 10>
Warning: Close contact of 2.219096 angstroms between .R<ASP 77>.A<HB2 6> and .R<WAT 465>.A<H2 2>
Warning: Close contact of 1.687677 angstroms between .R<PRO 86>.A<O 14> and .R<GLY 298>.A<H 2>
Warning: Close contact of 1.954963 angstroms between .R<ILE 88>.A<HD13 17> and .R<ILE 88>.A<H 2>
Warning: Close contact of 1.164720 angstroms between .R<TYR 96>.A<HH 15> and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.153334 angstroms between .R<TYR 96>.A<HH 15> and .R<THR 101>.A<OG1 11>
Warning: Close contact of 2.166421 angstroms between .R<TYR 96>.A<OH 14> and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.140836 angstroms between .R<GLN 108>.A<HE22 15> and .R<GLN 108>.A<HB3 7>
Warning: Close contact of 1.850847 angstroms between .R<GLN 110>.A<HE22 15> and .R<ASN 229>.A<HA 4>
Warning: Close contact of 1.823980 angstroms between .R<ARG 112>.A<HH11 18> and .R<HEM 357>.A<O1D 80>
Warning: Close contact of 1.339097 angstroms between .R<GLN 117>.A<HE21 14> and .R<WAT 433>.A<H1 1>
Warning: Close contact of 1.452897 angstroms between .R<ASP 125>.A<HA 4> and .R<WAT 496>.A<H2 2>
Warning: Close contact of 1.827194 angstroms between .R<ARG 130>.A<HD2 12> and .R<ARG 130>.A<HA 4>
Warning: Close contact of 1.762332 angstroms between .R<ILE 131>.A<HD13 17> and .R<ILE 162>.A<HD13 17>
Warning: Close contact of 1.785659 angstroms between .R<ALA 135>.A<HA 4> and .R<WAT 506>.A<H1 1>
Warning: Close contact of 1.668065 angstroms between .R<SER 141>.A<HB3 7> and .R<WAT 457>.A<H1 1>
Warning: Close contact of 1.648441 angstroms between .R<GLN 145>.A<H 2> and .R<WAT 448>.A<H2 2>
Warning: Close contact of 2.124973 angstroms between .R<GLY 146>.A<H 2> and .R<WAT 448>.A<O 3>
Warning: Close contact of 1.092559 angstroms between .R<GLY 146>.A<H 2> and .R<WAT 448>.A<H1 1>
Warning: Close contact of 1.790061 angstroms between .R<THR 151>.A<HG23 10> and .R<SER 258>.A<HG 9>
Warning: Close contact of 0.976382 angstroms between .R<THR 151>.A<HG21 8> and .R<THR 151>.A<H 2>
Warning: Close contact of 1.906989 angstroms between .R<LEU 165>.A<HB3 7> and .R<WAT 498>.A<H2 2>
Warning: Close contact of 0.839659 angstroms between .R<HID 176>.A<HD2 15> and .R<WAT 436>.A<H1 1>
Warning: Close contact of 2.184279 angstroms between .R<THR 181>.A<HG21 8> and .R<VAL 247>.A<HG23 14>
Warning: Close contact of 2.231917 angstroms between .R<ASP 182>.A<O 12> and .R<ARG 186>.A<H 2>
Warning: Close contact of 2.138727 angstroms between .R<MET 184>.A<HB3 7> and .R<PHE 193>.A<HE1 12>
Warning: Close contact of 1.731171 angstroms between .R<MET 191>.A<HE3 15> and .R<ALA 196>.A<HA 4>
Warning: Close contact of 1.620850 angstroms between .R<PHE 193>.A<HD2 18> and .R<WAT 487>.A<H1 1>
Warning: Close contact of 1.133502 angstroms between .R<ALA 194>.A<HA 4> and .R<WAT 487>.A<H2 2>
Warning: Close contact of 1.956045 angstroms between .R<GLU 209>.A<O 15> and .R<GLN 213>.A<HE22 15>
Warning: Close contact of 1.363557 angstroms between .R<ARG 211>.A<HH11 18> and .R<WAT 451>.A<H2 2>
Warning: Close contact of 2.188873 angstroms between .R<ARG 211>.A<HE 15> and .R<WAT 451>.A<H2 2>
Warning: Close contact of 2.117503 angstroms between .R<GLN 213>.A<HG3 10> and .R<GLN 213>.A<H 2>
Warning: Close contact of 2.164919 angstroms between .R<GLY 216>.A<H 2> and .R<SER 221>.A<HB3 7>
Warning: Close contact of 1.764190 angstroms between .R<ASP 218>.A<HA 4> and .R<WAT 517>.A<H2 2>
Warning: Close contact of 1.958026 angstroms between .R<ASN 229>.A<HD22 12> and .R<ASN 229>.A<HA 4>
Warning: Close contact of 2.120345 angstroms between .R<ILE 233>.A<HD11 15> and .R<GLU 237>.A<HB2 6>
Warning: Close contact of 1.722452 angstroms between .R<GLU 237>.A<O 15> and .R<MET 241>.A<H 2>
Warning: Close contact of 1.832649 angstroms between .R<GLU 237>.A<HG2 9> and .R<ARG 240>.A<HH21 21>
Warning: Close contact of 1.411345 angstroms between .R<VAL 247>.A<HG13 10> and .R<WAT 519>.A<O 3>
Warning: Close contact of 0.894151 angstroms between .R<VAL 247>.A<HG13 10> and .R<WAT 519>.A<H2 2>
Warning: Close contact of 2.083850 angstroms between .R<VAL 247>.A<HB 6> and .R<WAT 430>.A<H1 1>
Warning: Close contact of 1.873508 angstroms between .R<LEU 250>.A<HD23 17> and .R<WAT 428>.A<H1 1>
Warning: Close contact of 1.906005 angstroms between .R<ASP 251>.A<HA 4> and .R<WAT 472>.A<H2 2>
Warning: Close contact of 2.228194 angstroms between .R<VAL 254>.A<HB 6> and .R<WAT 472>.A<H1 1>
Warning: Close contact of 1.976005 angstroms between .R<ASN 255>.A<H 2> and .R<WAT 472>.A<O 3>
Warning: Close contact of 0.438342 angstroms between .R<ASN 255>.A<H 2> and .R<WAT 472>.A<H1 1>
Warning: Close contact of 2.120191 angstroms between .R<SER 267>.A<HA 4> and .R<PRO 268>.A<HD2 3>
Warning: Close contact of 1.968942 angstroms between .R<LEU 274>.A<HD23 17> and .R<ILE 281>.A<HD11 15>
Warning: Close contact of 0.246143 angstroms between .R<ARG 277>.A<HH21 21> and .R<ARG 280>.A<HH21 21>
Warning: Close contact of 2.248835 angstroms between .R<ARG 277>.A<HH21 21> and .R<ARG 280>.A<NH2 20>
Warning: Close contact of 1.353690 angstroms between .R<ARG 277>.A<NH2 20> and .R<ARG 280>.A<HH21 21>
Warning: Close contact of 0.711629 angstroms between .R<ALA 283>.A<H 2> and .R<WAT 513>.A<H2 2>
Warning: Close contact of 2.110204 angstroms between .R<ARG 290>.A<HH11 18> and .R<ARG 290>.A<HD2 12>
Warning: Close contact of 1.929369 angstroms between .R<LEU 294>.A<H 2> and .R<WAT 515>.A<H1 1>
Warning: Close contact of 0.654612 angstroms between .R<VAL 295>.A<H 2> and .R<WAT 515>.A<H2 2>
Warning: Close contact of 1.399941 angstroms between .R<GLY 298>.A<O 7> and .R<ARG 299>.A<HH11 18>
Warning: Close contact of 1.998699 angstroms between .R<GLY 298>.A<O 7> and .R<ARG 299>.A<HD3 13>
Warning: Close contact of 1.251292 angstroms between .R<ARG 299>.A<HE 15> and .R<WAT 474>.A<H2 2>
Warning: Close contact of 2.095108 angstroms between .R<LYS 313>.A<HE2 15> and .R<WAT 488>.A<H2 2>
Warning: Close contact of 1.964478 angstroms between .R<LYS 313>.A<HE2 15> and .R<WAT 504>.A<H1 1>
Warning: Close contact of 1.597401 angstroms between .R<GLN 322>.A<HE22 15> and .R<WAT 491>.A<H2 2>
Warning: Close contact of 2.212426 angstroms between .R<ARG 330>.A<HH21 21> and .R<WAT 452>.A<H2 2>
Warning: Close contact of 1.902618 angstroms between .R<ALA 334>.A<H 2> and .R<WAT 485>.A<H1 1>
Warning: Close contact of 2.201433 angstroms between .R<HEM 357>.A<HBM 61> and .R<HEM 357>.A<HV4 55>
Warning: Close contact of 2.241537 angstroms between .R<ARG 365>.A<HH22 22> and .R<WAT 526>.A<H2 2>
Warning: Close contact of 2.102031 angstroms between .R<ARG 365>.A<HH11 18> and .R<ARG 365>.A<HD2 12>
Warning: Close contact of 2.167108 angstroms between .R<GLU 373>.A<OE1 12> and .R<ARG 377>.A<HH12 19>
Warning: Close contact of 1.392790 angstroms between .R<GLU 373>.A<HG2 9> and .R<GLU 373>.A<H 2>
Warning: Close contact of 1.782277 angstroms between .R<ILE 389>.A<HD13 17> and .R<ILE 389>.A<H 2>
Warning: Close contact of 1.732702 angstroms between .R<WAT 426>.A<H1 1> and .R<WAT 436>.A<H2 2>
Warning: Close contact of 1.778697 angstroms between .R<WAT 429>.A<H2 2> and .R<WAT 517>.A<H1 1>
Checking parameters for unit 'mol'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 82
Unit is OK.
> saveamberparm mol 2h7s.crd 2h7s.top
Checking Unit.
WARNING: The unperturbed charge of the unit: -20.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HEM 357>:  -M   CA   N    H   
 <HEM 357>:  CA   +M   C    O   
 <HEM 357>:  NA   C1A  C4A  FE  
 <HEM 357>:  NB   C1B  C4B  FE  
 <HEM 357>:  NC   C1C  C4C  FE  
 <HEM 357>:  ND   C1D  C4D  FE  
 <HEM 357>:  C1A  C2A  NA   CHA 
 <HEM 357>:  C1B  C2B  NB   CHB 
 <HEM 357>:  C1C  C2C  NC   CHC 
 <HEM 357>:  C1D  C2D  ND   CHD 
 <HEM 357>:  C2A  C3A  C1A  CAA 
 <HEM 357>:  C2B  C3B  C1B  CMB 
 <HEM 357>:  C2C  C3C  C1C  CMC 
 <HEM 357>:  C2D  C3D  C1D  CMD 
 <HEM 357>:  C3A  C4A  C2A  CMA 
 <HEM 357>:  C3B  C4B  C2B  CAB 
 <HEM 357>:  C3C  C4C  C2C  CAC 
 <HEM 357>:  C3D  C4D  C2D  CAD 
 <HEM 357>:  C4A  NA   C3A  CHB 
 <HEM 357>:  C4B  NB   C3B  CHC 
 <HEM 357>:  C4C  NC   C3C  CHD 
 <HEM 357>:  C4D  ND   C3D  CHA 
 <HEM 357>:  C4D  C1A  CHA  HGM 
 <HEM 357>:  CAC  HT3  CBC  HC4 
 <HEM 357>:  C3C  CBC  CAC  HV4 
 <HEM 357>:  CAB  HT7  CBB  HC8 
 total 1310 improper torsions applied
 26 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.