It was hidden in the length of my previous response, but I did actually
answer that ;) --
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.
See section 10.3.4, the second type of calculation. You can look at
$AMBERHOME/AmberTools/test/mmpbsa_py/08_Stability for example system setups
that run stability calculations.
Note that you *can* use idecomp in sander directly (that is what MMPBSA.py
does), but I think the results are parsed and displayed more efficiently
with MMPBSA.py.
HTH,
Jason
On Thu, Jul 19, 2012 at 10:58 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> 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
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > _______________________________________________
> >> > 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 20:30:02 PDT
