This can be deduced from the standard Amber force field equation (
http://en.wikipedia.org/wiki/AMBER which is oversimplified and not quite
correct since it doesn't account for 1-4 nonbonded scaling and nonbonded
exclusions). The summations run over all atoms. Thus, any potential terms
that involve any of the atoms of a particular residue is included in that
residue's energy decomposition. For pairwise decomposition, only the terms
that have one atom from the first residue and another atom from the second
residue are included.
Note this becomes a bit ambiguous when it comes to decomposing the
solvation free energy terms (like generalized born or poisson boltzmann).
In this case (GB), the pairwise energy terms are calculated, but the
effective radii are determined from every atom in the system.
HTH,
Jason
On Tue, Jan 24, 2012 at 11:53 AM, Anglea A. <a.anglea90.yahoo.com> wrote:
> Dear AMBER
> I was wondering if you could direct me to the equation or the idea behind
> the energy decomposition (pairewise/per-residue) in amber.
> Cheers
>
> _______________________________________________
> 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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Received on Tue Jan 24 2012 - 10:30:03 PST
