Re: [AMBER] MM-GBSA for recptor-magnesium-ligand complex

From: Urszula Uciechowska <>
Date: Wed, 13 Jun 2018 15:07:36 +0200


I checked the sander complex file and mmpbsa complains about the atom
mismatch, I do not really understand why there is an atom mismatch? How
to check where this mismatch is and correct it? I am quite sure that the
topology and crd files are correct? Could the magnesium ion cause the

INFO: Old style inpcrd file read

  FATAL: NATOM mismatch in coord and topology files

Thank you in advance for any suggestions


> On Thu, Jun 07, 2018, Urszula Uciechowska wrote:
>> CalcError: /users/work/czarek/amber16/bin/sander failed with prmtop
>> Error occured on rank 0.
>> Exiting. All files have been retained.
> You need to look at the sander output file(s) to get a better idea of
> what the problem is. It will be in the run that used the complex
> trajectory.
> ...good luck....dac
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> AMBER mailing list

Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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Received on Wed Jun 13 2018 - 06:30:03 PDT
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