Dear Amber Users,
I am trying to prepare amber input files for Cytochrome P450.
When I tried to save to topology file and coordinate file, following
message appears. After "Marking per-residue atom chain types." System
gets stuck. It didn't create any topology file. What will be the
possible reason for this error. I will be grateful for your suggestion.
Thanks
Abdul Rajjak
> saveamberparm mol parmtop parmcrd
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.
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Received on Wed Oct 08 2008 - 05:13:26 PDT
