On Fri, Apr 8, 2016 at 12:14 AM, 楊承翰 <u16chy01.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to calculate the binding energy and keeping explicit water
> molecules with MMPBSA( amber14 and ambertools15 ).
>
Keeping all explicit water molecules defeats the purpose of MM/PBSA. If
you just want to keep a few water molecules because they are structurally
important, that is challenging if they are not conserved. Basically,
you'll have to use cpptraj to pre-process the trajectory in order to keep
the water molecules you want (using, for instance, the "closest" command
perhaps). Then do not allow MMPBSA.py to strip solvent (i.e., by not
passing in a -sp flag).
I would suggest running this calculation by hand first to make sure you
know how to do it. Once you can see how to get MMPBSA.py to do the same
thing, you can use the script to save time. But this is an example where
running it as a black box can hide useful and important information.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Apr 08 2016 - 05:30:05 PDT
