Hello,
Is it possible to add some provision for doing group decomposition in
future versions of MMPBSA.py ?. All I meant is, to sort out the already
decomposed (pair-wsie) different energy terms based on different group of
residues that read as input from mmpbsa.in, i.e. say between group 1 ( RES
1 10) and group 2 (RES 200 250).
Best regards
Anu
On Thu, Aug 20, 2015 at 2:21 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Hi Jason,
>
> I full agree, the attached files are meant just to learn.
>
> Regards,
> Hector.
>
>
> > On Thu, 2015-08-20 at 09:09 -0300, Hector A. Baldoni wrote:
> >> Hi Anu,
> >>
> >> Attached you will find some in/out files about how to calculate the
> >> interaction energies between protein-K+ using anal. You could download
> >> anal software, compile and learn from the attached file how to use it.
> >> I hope this will help you.
> >
> > But this does not address Dave's points about the lack of pairwise
> > decomposability of the GB and PME potential energy functions.
> >
> > Sure, anal will give you something it *calls* an interaction energy, but
> > that interaction energy will be a simple, gas-phase (maybe with an
> > aphysical, distance-dependent dielectric) interaction that bears little
> > resemblance to the potential energy function you actually run
> > simulations with these days.
> >
> > In particular, the interaction between surface atoms of the two species
> > is treated exactly the same as the interaction between two buried atoms
> > near the interface. In a solvated environment, this is clearly the
> > wrong thing to do if what you are interested in is the interaction
> > energy in solution.
> >
> > The challenge here is that the GB and PME potentials -- which account
> > for solvation effects in a more physically sensible model -- are not
> > pairwise decomposable, so the anal approach will not work here. You
> > need something different.
> >
> > For GB, the "pairwise decomposition" coded in sander treats the
> > effective GB radii as a "constant" derived from the calculated effective
> > radii of the entire system (when in reality the radii differ between the
> > "bound" and "unbound" complexes). This approximation makes the GB
> > potential pairwise decomposable. While approximate, it is almost
> > certainly better than what anal does.
> >
> > For PME, the reciprocal sum is definitely not pairwise decomposable, and
> > pair interaction energies need to be calculated by performing 3 separate
> > nonbonded energy calculations -- one with the full system, one in which
> > only the first part of the pair has nonzero nonbonded terms, and one in
> > which only the second part of the pair has nonzero nonbonded terms. You
> > still get contributions from the periodic images, so it's still an
> > approximation, but it's significantly better than what anal did.
> >
> > I'd not suggest using anal for this purpose. The idecomp=3/4 option in
> > sander and the 3-calculation PME approach are substantially better, and
> > may give results that are even qualitatively different from what anal
> > gives.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --------------------------------------
> Dr. Hector A. Baldoni
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
>
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Received on Wed Aug 26 2015 - 10:30:03 PDT
