On Sat, Dec 15, 2012 at 7:23 AM, RANAJIT SHINDE <
science.ranajitshinde.gmail.com> wrote:
> Dear AMBER users,
>
>
> I performed per-residue decomposition analysis using python script in
> AMBER11. A hydrogen bond between sulfonamide nitrogen (acceptor) of
> inhibitor and carboxylic oxygen (donor) of aspartic acid residue was
> consistent throughout the simulation of 25 ns (Average distance 2.82
> angstrom). However, higher value was observed for polar solvation term than
> the electrostatic contribution term which led hydrogen bond as unfavorable
> interactions. Following are the details of calculation.
>
Keep in mind that the per-residue decomposition includes contributions from
each residue to every other residue. Therefore, while I would expect a
hydrogen bond to be overall stabilizing in the electrostatic/polar
solvation terms, that doesn't mean that other residues don't destabilize it.
You can do a quick pairwise decomposition calculation in which you only
print the two residues who are interacting, to convince yourself that the
two interact favorably. In this case, however, take note that implicit
solvent methods are not pairwise decomposable, since the dielectric
boundary is non-local quantity calculated from the entire system. In the
case of GB, the effective Born radii are calculated as a double-sum over
all atom pairs -- after which these radii are used in the GB equation that
'appears' to be pairwise decomposable.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Dec 15 2012 - 05:30:02 PST
