Re: [AMBER] Per-residue decomposition energy

From: maryam azimzadehirani <>
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 <>

> On Mon, 2015-03-16 at 21:49 +0800, maryam azimzadehirani wrote:
> > Dear all,
> > Can anyone simply explains to me how 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
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Received on Mon Mar 16 2015 - 21:00:02 PDT
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