I'm sure it's possible to do with AMBER, but maybe perhaps not with
MMPBSA.py (I'm not an expert with that program and have always done my
calculations "by hand"). The hard part will be retaining the right number
of water molecules for each frame. I've not heard of retaining water in
such calculations, and without any details, I'm not sure how you would
account for them properly in the bound and unbound states. This probably
requires a survey of the literature via google or whatever other source you
prefer.
Regards,
Brian
On Tue, Aug 5, 2014 at 3:19 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir,
> I have a nucleic acid ligand system with negatively charged ligand.
> (mimor groove binding) cooH group protrude out of the groove. i would
> like to do an mmpbsa calculation retaining certain amount of water
> shell around the complex. Is it possible to do so? is there any
> reference papers available in this regard?
>
>
> thankimg you
> mary
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Tue Aug 05 2014 - 08:00:03 PDT
