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.
By all means, someone else tell me if I am wrong.
Hope this helps a little bit.
-Hunter Brown
-----Original Message-----
>From: Shashidhar Rao <shashidharr.gmail.com>
>Sent: Jul 25, 2013 8:49 PM
>To: AMBER Mailing List <amber.ambermd.org>
>Subject: [AMBER] MMPBSA.py
>
>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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Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
University of New Mexico
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Received on Fri Jul 26 2013 - 08:00:06 PDT
