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 Thu Jul 25 2013 - 20:00:03 PDT
