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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>
--
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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Received on Thu Jul 25 2013 - 20:30:02 PDT
