> On Jan 12, 2015, at 11:25 AM, zahra khatti <zkhatti2000.yahoo.com> wrote:
>
> For example for visualizing electrostatic potential map in vmd,I didn't see any option in mmpbsa.py; but there is in pbsa.
But you had said you wanted to plot van der Waals and binding free energies -- those can be done with MMPBSA.py (well, not the plotting part). This option is unrelated to your original question as far as I can tell?
I’m not sure what question you are trying to ask here: if MMPBSA.py doesn’t do something you want, you can’t use it for that. If it does do what you want, you can use it. Same goes for PBSA (or any other Amber program).
A general rule of thumb is that if something doesn’t relate directly to calculating energies, MMPBSA.py is probably not the right tool.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 12 2015 - 09:00:03 PST
