many thanks to all of you who provided feedback on this matter. the issue
is cleared up for me.
cheers,
Shashi Rao
On Fri, Jul 26, 2013 at 3:36 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Sun Jul 28 2013 - 06:30:04 PDT
