AMBER Archive (2008)

Subject: RE: AMBER: saveamberparm error

From: Ross Walker (
Date: Wed Oct 08 2008 - 10:23:12 CDT

Dear Shaikh,


I don't see any error message in your output below. What exactly do you mean
by the "System gets stuck"? Does it just hang at this point?


Can you send us your full set of leap commands, I.e. what you did before the
saveamberparm, as well as a more in-depth discussion of the pdb you used,
how you modified it, what parameters you are using etc. and then we might be
able to work out what is going on.


All the best



From: [] On Behalf Of
Shaikh Abdul R S Ramaju
Sent: Wednesday, October 08, 2008 4:34 AM
Subject: AMBER: saveamberparm error


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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