Dear Prof. Case,
Thank you very much for letting me know your valuable comments on a
non-polar contribution for PBSA method.
If I have an opportunity, I would like to exam the MM-RISM method for
further evaluation.
Thanks a lot.
Best wishes,
Keigo
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Tuesday, March 10, 2015 8:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA tutorial: MMPBSA.py
On Tue, Mar 10, 2015, camm-kansai wrote:
>
> MMPBSA calculation using the modified mmpbsa.in for MMPBSA.py gave quite
> identical results to that of mmpbsa_pl, i.e., -87.82 kcal/mol, which seems
> to resolve my issue. However, by looking at the AMBER14 manual, it says
that
> inp=1 is an old method for nonpolar optimization.
We should update the manual. It *is* true that inp=1 is older than inp=2,
but
that doesn't mean it is less reliable. My sense is that inp=2 is sometimes
OK
(as in the cases analyzed in the papers that describe how it was
constructed),
but that for other cases it has unexpected weaknesses. As a default, inp=1
seems a better choice in the sense that it is more uniformly applicable.
One of the problems with almost all PBSA-based schemes is the need to
specify
a non-polar contribution, and it is hard to get one that is really good.
MM-RISM is an attractive alternative, but has never been tested to nearly
the
same extent as MM-PBSA.
....dac
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Received on Fri Mar 13 2015 - 06:30:02 PDT
