On Mon, Oct 3, 2011 at 3:30 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> 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.
>
What do the standard deviations of the differences come out to be? The real
term I would suggest looking at is the sum of EEL and EGB (since they're
really just 2 parts of the same calculation). I would also suggest trying
the PB solvation method (perhaps even using the non-linear equation) as an
improved level of theory. However, I think that just tossing residues out
on a whim isn't the best way of going about things.
Others may have other advice.
HTH,
Jason
>
> 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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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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 Mon Oct 03 2011 - 13:00:04 PDT
