Re: [AMBER] Periodicity errors in pymdsapb

From: case <>
Date: Mon, 14 May 2012 17:54:04 -0400

On Mon, May 14, 2012, Genzo Tanaka wrote:
> A periodicity error occurred during a calculation for the free energy of
> binding in pymdpbsa using a molecular dynamics file from mdnab:
> % pymdpbsa --proj=test,--traj=traj.binpos,--cprm=com.prm,--lprm=lig.prm,
> --rprm=rec.prm,lig=flmfoh1,--start=1,--stop=1000,--step=200,--solv=1,
> --clean &
> % Found an invalid periodicity in the prmtop file: 5

This is a fatal error that will cause everything after it to fail. It's not
clear (to me, anyway) which prmtop file was being read when the error occured.
But you should look at all three prmtops: go to the DIHEDRAL_PERIODICITY
section, and look at the 6th number (the count starts from 0): that number
is probably zero, which is not a valid value for the periodicity.

This just starts to localize the problem, but maybe it will help. For
example, you can see which prmtop file is the problem, and which atoms are
involved -- is perhaps the fluorine, where you have your own parameters (I
guess)? Are there also any zero entries for DIHEDRAL_PERIODICITY in any of
the other prmtop files? Basically, we have to find out how/why this entry was
created, in order to have enough information to try to fix it.

...good luck...dac

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Received on Mon May 14 2012 - 15:00:02 PDT
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