Re: [AMBER] binding free energy

From: David A Case <>
Date: Thu, 15 Mar 2012 08:51:43 -0400

On Tue, Mar 13, 2012, kirtana S wrote:

> Found an invalid periodicity in the prmtop file: 0

This error message has nothing to do with mmpbsa or with gb. It is a check
in the NAB version of the prmtop reader that (I think?) is not replicated in
sander or pmemd. It does indicate that something funny is going on with your
prmtop file: at the least, NAB is having trouble reading it. I think we would
need to know more about what sort of system this is, and how you made the
prmtop file. There may some context that indicates which of the several
prmtop files mmpbsa deals with is being read....


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Received on Thu Mar 15 2012 - 06:00:05 PDT
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