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From: maryam azimzadehirani <maryamai1988.gmail.com>

Date: Tue, 17 Mar 2015 11:52:58 +0800

That was really helpful. Thanks. I was unaware of R (effective radii) as a

sum for all atoms. I need to read more on this.

On Mon, Mar 16, 2015 at 10:26 PM, Jason Swails <jason.swails.gmail.com>

wrote:

*> On Mon, 2015-03-16 at 21:49 +0800, maryam azimzadehirani wrote:
*

*> > Dear all,
*

*> > Can anyone simply explains to me how MMGBSA.py calculates per-residue
*

*> > decomposition energy?
*

*> > I assume it is similar to binding energy calculation where it calculates
*

*> > the free energy of ligand (solvated and in vacuum), free energy of
*

*> receptor
*

*> > (solvated and in vacuum) and ligand-receptor free energy (solvated and in
*

*> > vacuum). Then calculate Gibbs free energy of binding, as they mentioned
*

*> in
*

*> > advance tutorial 3:
*

*>
*

*> Loosely speaking, this is almost equivalent to what happens.
*

*>
*

*> > If we don't talk about entropy at all, which makes everything
*

*> confusing...
*

*> > In a simple way, the same method is used for each residue in per-residue
*

*> > decomposition calculation, where the whole ligand is replaced by each
*

*> > residue that we chose in the mask?
*

*>
*

*> No, this is not what happens. This would be more "correct" than what is
*

*> currently done (I enclose in quotes since you would need to
*

*> appropriately handle the dangling valences caused by cutting residues
*

*> out of the polymer chain and then account for the extra atoms you needed
*

*> to add to cap that valence... it would be challenging, not to mention
*

*> expensive, to do that "correctly").
*

*>
*

*> What's done in reality for MM/GBSA pairwise decomposition is much
*

*> simpler: the formula for GB free energies is a pairwise sum (see
*

*> equation 4.2 in the Amber 14 manual on page 57, along with Equation
*

*> 4.3). The sum is actually a double-sum (and the 1/2 accounts for
*

*> including both i->j and j->i in the sum).
*

*>
*

*> You can imagine based on this formula calculating the "contribution" to
*

*> the total energy for each atom (or for pairwise decomposition, for each
*

*> atom pair). Then, all you do is add up the energies for each atom in a
*

*> particular residue to get the "per-residue" decomposed energy.
*

*>
*

*> This is rigorously correct if you have a truly pairwise potential energy
*

*> function. While Eq. 4.2 looks that way at first glance, the term R (see
*

*> Eq. 4.5) is itself a sum over all atom pairs as well... which means that
*

*> the GB energy function is *not* pairwise decomposable. But the
*

*> resulting decomposition can be qualitatively useful.
*

*>
*

*> HTH,
*

*> Jason
*

*>
*

*> --
*

*> Jason M. Swails
*

*> BioMaPS,
*

*> Rutgers University
*

*> Postdoctoral Researcher
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Mon Mar 16 2015 - 21:00:02 PDT

Date: Tue, 17 Mar 2015 11:52:58 +0800

That was really helpful. Thanks. I was unaware of R (effective radii) as a

sum for all atoms. I need to read more on this.

On Mon, Mar 16, 2015 at 10:26 PM, Jason Swails <jason.swails.gmail.com>

wrote:

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Received on Mon Mar 16 2015 - 21:00:02 PDT

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