From: Jason Swails <>
Date: Thu, 18 Sep 2014 12:27:17 -0400

On Thu, 2014-09-18 at 21:38 +0530, Sourav Purohit wrote:
> Thanks for the suggestions.
> So is there some way to know which are the frames of the trajectory file
> that are causing the problem, or how many frames are being rejected.
> Finally I get an output and a number for entropy change but don't know
> whether to believe the number or not. Some comments on these please.

The entropy is computed only for snapshots that minimize to within the
requested tolerance.

Look at the _MMPBSA_complex_nm.out.X files (and those for the receptor
and ligand as well) for the full output of those calculations. You
should be able to tell from those output files which (if any) snapshots
failed to minimize to within your requested tolerance.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 18 2014 - 09:30:06 PDT
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