Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Tue, 30 Apr 2013 12:51:27 +0200

On 04/30/2013 12:06 PM, Jan-Philip Gehrcke wrote:

> Much larger numbers here in case of AT 13. Is that expected behavior? Or
> does something go wrong in the MMPBSA run with the inp=1 setting?
>

In the PBSA manual section I read that inp=1 requires use_sav=0. There
is a default defined for sander in /MMPBSA_mods/pb.py. It's use_sav=1. I
found no further occurrence of use_sav in the MMPBSA sources using grep.
Since use_sav is 1 by default in PBSA, it should be explicitly set to 0
by MMPBSA in case of the MMPBSA pb namelist setting inp=1, right? I'll
try to test how this is related to the numbers I have observed.

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Received on Tue Apr 30 2013 - 04:00:03 PDT
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