On Fri, Sep 30, 2011 at 5:02 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> hi all
>
> I have a completed MD trajectory. I'd like to perform binding free energy
> calculation with MMPBSA (python version, ambertool1.5). However, I'd like
> to
> include only residues within a certain range of the ligand. How can I do
> that? Thanks a lot.
>
You can't automatically with either version of MMPBSA.py. The only way you
can do this is if you strip out every atom/residue that you *don't* want and
create a new topology from that (I wouldn't suggest this method, since there
will probably be issues arising from converting free-floating residues into
termini, etc.).
The closest you can really come is one of the decomposition schemes (and be
clever about how you add the terms up), but you won't actually save any time
doing it this way (in fact it will take a lot longer). For entropy, there's
no way to do this automatically (we may think about implementing Ryde's
approach or something similar later, but that's not on the radar for right
now).
HTH,
Jason
> Victor
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 30 2011 - 17:00:03 PDT
