On Jul 28, 2013, at 9:17 AM, Shashidhar Rao <shashidharr.gmail.com> wrote:
> 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?
If there are specific waters that you need, you can just set strip_mask in the &general section to the mask required to delete all the unnecessary waters and keep those you want.
If the waters that you need to keep are different each frame, you may need to preprocess the trajectory using something like the "closest" command in cpptraj before using MMPBSA.py.
HTH,
Jason
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Received on Sun Jul 28 2013 - 09:30:03 PDT
