Thank you Jason for the remarks. Indeed what I am looking for is just
a qualitative representation of the pairwise interactions. As for
Carlos' response, I am using amber 12. I have taken a look again at
the manual and found that the idecomp flag description is within the
MMPBSA section of the ambertools manual. In this case I'll need to
strip out the solvent and ion molecules from my simulation, right? In
this case, I do not have any actual ligands to specify, but rather a
list of protein residues that I want to monitor. Would this be valid
input for MMPBSA or is the fact that the ligand is part of the protein
a problem?
Thank you
Fabrício
2012/7/19 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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 - 20:00:03 PDT
