Re: [AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!

From: David A Case <>
Date: Tue, 10 Mar 2020 14:44:31 -0400

On Tue, Mar 10, 2020, Harold Grosjean wrote:
>I am trying to perform MMGBSA calculation on a simulation of a
>protein-ligand system. When I try to run the command on my
>terminal - the error bellow is returned.
>My "master" topology file was translated with gromber and then "stripped"
>with: -p complex.prmtop -c prot-lig-ant2.prmtop -r
>prot-ant2.prmtop -l lig-ant2.prmtop -s :CL:NA:SOL -n :LIG
>The VERY strange thing is that the calculation runs without problems when
>the "use_sander=1" is present in my file. The following error
>appears when I remove it,
>*Found an invalid periodicity in the prmtop file: 285*

Sander is indeed more flexible in allowing non-standard periodicities
than are the sff routines (or maybe cpptraj routines) that would
otherwise be used.

That said, if you indeed have a periodicity of 285, that is clearly an
error. I'm guessing that this came about via gromber, and not from (although who knows?)

You will probably have to either use a text editor or the ParmEd program
to examine your prmtop file to see if you can locate the problem entry.
One can hope that doing this will provide some clue about what is going


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Received on Tue Mar 10 2020 - 12:00:02 PDT
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