AMBER Archive (2008)

Subject: AMBER: saveamberparm error

From: Shaikh Abdul R S Ramaju (
Date: Wed Oct 08 2008 - 06:33:31 CDT

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.



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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