use_sav should be getting reset to 0 if inp==1 (see line 1020 in
pb_read.F90). If you force MMPBSA.py to use sander, do you see the warning:
'PB Warning in pb_read(): the cavity energy should be correlated
to &
& the SASA when inp=1, so use_sav is reset to 0.'
written anywhere in your mdout files?
Unfortunately I really don't know what could be causing this discrepancy,
since I'm not intimately familiar with PBSA development.
All the best,
Jason
On Tue, Apr 30, 2013 at 6:51 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 30 2013 - 05:30:03 PDT
