On Fri, Jul 26, 2013 at 10:39 AM, Hunter Brown <bassoongoon.earthlink.net>wrote:
> MMPBSA.py requires three (usually four I think) prmtop files. The best way
> to prepare those is in LEaP. If I recall, the manual, and MMPB(GB)SA
> tutorial describe the usage quite nicely. If I recall correctly, an the
> MDCRD does not (and indeed should not?) need to be stripped of waters.
>
You can either have MMPBSA.py strip waters for you (in which case, you must
provide a solvated prmtop file via the -sp flag). Or you can strip it
beforehand (in which case, the solvated prmtop file must be omitted).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 26 2013 - 13:00:08 PDT
