oh I didn't realize it was added. Thanks for the reply :)
On Sat, Feb 16, 2013 at 3:24 PM, Jason Swails <jason.swails.gmail.com>wrote:
> I hadn't thought much about how the normal mode entropy would be
> decomposed, but decomposition support was added to the nmode program in
> 2009. I believe mm_pbsa.pl supports normal mode entropy decomposition,
> but
> I have never used it (and never even looked into it).
>
> Look at the Amber 12 manual for more instructions (mm_pbsa.pl). The code
> is pretty straightforward ($AMBERHOME/src/nmode/decomp.F90), so you should
> be able to figure out how the contribution for each normal mode (vector) is
> attributed to each residue.
>
> HTH,
> Jason
>
> On Sat, Feb 16, 2013 at 1:06 PM, Aron Broom <broomsday.gmail.com> wrote:
>
> > Hi AMBER users,
> >
> > I'm wondering if it is theoretically possible to decompose the entropy
> term
> > from an MM PBSA/GBSA calculation to determine the contribution of each
> > residue?
> >
> > I realize the script currently does not support this, and the manual
> makes
> > that quite clear. I also believe I understand that in taking in the
> whole
> > complex there would be no way to actually do this decomposition easily.
> > What I'm wondering is, from a theoretical perspective, if one did the
> > normal alignment of the whole complex to remove those irrelevant
> rotations
> > and translations, and then stripped out all but the residue of interest,
> > and performed the entropy calculations (Quasi-harmonic or nmode) on just
> > that reduced trajectory (which has been pre-aligned as part of the whole
> > complex), would you get something sensible? That is, would doing this
> for
> > each residue give a final result that more or less added up to what you
> > would get from doing the whole complex (I realize there is a lot of
> > uncertainty in entropy calculations as it is, and so there would be a
> > tremendous propagation of error involved)?
> >
> > I'm asking about this because MM/PBSA calculations seem to offer a very
> > nice advantage over other methods for determining say ligand binding
> energy
> > (umbrella sampling, thermodynamic integration etc..) in that one can get
> > these per residue decompositions of the energy terms, and thereby get a
> > clue as to how the protein for instance, might be re-engineered for
> better
> > binding, whereas methods like umbrella sampling would essentially
> require a
> > guess, followed by another whole analysis of the mutated complex in order
> > to test only one potential mutation.
> >
> > Thanks,
> >
> > ~Aron
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Feb 16 2013 - 13:30:02 PST
