You could decompose the energies with no periodicity even if originally run
with pme- the key thing really is whether you want just the coulomb
energy, or some estimate of solvent contributions.
On Jul 19, 2012 9:57 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> As Carlos mentioned, you should try the "idecomp" flag to get what you
> want. The problem with decomposing into pairwise interactions within a
> system is that no potential energy functions that Amber uses are truly
> pairwise decomposable for the electrostatic contributions.
>
> In implicit solvent, the dielectric boundary is defined by every atom in
> the system, and since the solvation term depends on the definition of this
> boundary (to distinguish between a 'buried' and 'exposed' residue),
> interactions between 'pairs' of atoms or residues in this context will
> include contributions from all other atoms in the system via the
> calculation of the effective Born radii (GB) or the dielectric switching
> function (PB). Furthermore, by using an implicit solvent model, you're
> including the screening effects of the solvent molecules surrounding your
> protein in your pairwise interaction.
>
> This type of decomposition is available through MMPBSA.py on a single
> structure via a 'stability' calculation. If you want to know how two
> protein residues interact, this is the route I suggest. ante-MMPBSA.py
> will set up stripped topology files for you to run MMPBSA.py with.
>
> Explicit solvent (PME) carries with it a completely different set of
> limitations. In Ewald sums, the electrostatic interaction is divided into
> a short-range term and a long-range term (the first summed via a direct
> sum-over-nearby-pairs and the latter summed in reciprocal space using a
> FFT). The reciprocal space term in general is not pairwise decomposable
> (I've been told you can play tricks, but it's not straightforward nor is it
> implemented in Amber), and the direct-space sum is meaningless without it
> (since it is artificially dampened with a neutralizing gaussian counterion
> to reduce the required cutoff, and the effect of this artificial counterion
> is reversed in the reciprocal space part). A quick glance at the code
> suggests there is no decomposition accumulation in the reciprocal space
> part, so I'm not even sure how you would interpret decomposed energies in
> explicit solvent...
>
> Perhaps someone can clear up that last point for me if there is a
> meaningful interpretation. In any case, I assert (perhaps incorrectly)
> that pairwise-decomposed energies can be qualitatively helpful, but should
> be taken with a grain of salt.
>
> HTH,
> Jason
>
> On Thu, Jul 19, 2012 at 6:21 PM, Irene Newhouse <einew.hotmail.com> wrote:
>
> >
> > I'm EXTREMELY interested in being able to do this myself! Someone please
> > tell! Irene Newhouse
> > > Date: Thu, 19 Jul 2012 18:47:25 -0300
> > > From: bracht.iq.ufrj.br
> > > To: amber.ambermd.org
> > > Subject: [AMBER] Interaction energy between residue pairs
> > >
> > > Hello. If one had a molecular dynamics simulation of a solvated
> > > protein (in this case, water is the solvent), and was interested in
> > > retrieving VdW and Coulomb interaction energies between pairs of
> > > residues (very specific pairs of residues. Just in case you are
> > > wondering, there are no ligands, just protein residues) for this
> > > particular simulation. What would be the best way to do this in Amber?
> > > The idea here is see the effect that a mutated residue has in one(or
> > > more) of the catalytic site residues.
> > > Thank you
> > > Fabrício Bracht
> > >
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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 Thu Jul 19 2012 - 19:30:02 PDT
