Hello Dwight,
many thanks for your response and I apologize for not responding sooner.
it is good to note that MMPBSA.py strips all waters and ions by default.
however, in a specific situation where I wanted to retain some water
molecules in the active site, I would assume that I would use cpptraj? is
that right?
thanks,
shashi rao
On Thu, Jul 25, 2013 at 11:05 PM, Dwight McGee <dwight.mcgee.gmail.com>wrote:
> Hi,
>
> By default MMPBSA.py strips all waters and ions from the trajectories it
> reads in, so there is no need to preprocess your trajectories in your
> particular case.
>
>
> On Thu, Jul 25, 2013 at 10:49 PM, Shashidhar Rao <shashidharr.gmail.com
> >wrote:
>
> > Hello AMBER Gurus,
> >
> > I apologize for asking a very naive question. I have carried out AMBER
> MD
> > studies on a series of protein-ligand complexes and would like to carry
> out
> > MMGB-SA and MMPB-SA calculations on the trajectories. my system
> includes a
> > box of waters in addition to the protein-ligand complex as well as the
> > counterions. I wanted to know if the MMPBSA.py script can be run on the
> > trajectories as they are or do I need to take out the waters and the
> > counterions. If latter, what is the best way to do so (perhaps cpptraj)?
> >
> > thanks for your help in advance,
> > Shashi Rao
> >
> > --
> > Shashidhar N. Rao
> > 3 SERINA DRIVE
> > PLAINSBORO
> > NEW JERSEY 08536 USA
> >
> > shashidharr.gmail.com
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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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
