Thanks Jason. I am working on a highly charged system. When doing MMPBSA, I
typically get a EEL, EGB of ~ 30-50K kcal/mol for the complex and receptor
system and a difference of ~1-3K kcal/mol. That gives me a too large margin
of uncertainty in the free energy calculation. So besides extracting some
residues out of the trajectory, do you have any other suggestions? Thanks a
lot.
Victor
On Fri, Sep 30, 2011 at 6:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Mon Oct 03 2011 - 13:00:03 PDT
