No need to remove water tou can perform the calculations using water
On 26 Jul 2013 08:19, "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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Received on Fri Jul 26 2013 - 08:00:07 PDT
