Re: [AMBER] MMPBSA: question of pairwise per residue decomposition

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 5 May 2016 09:09:26 -0400

On Thu, May 5, 2016 at 6:23 AM, George Tzotzos <gtzotzos.me.com> wrote:

> Thank you Jason
>
> Given that vdi + Electrostatic = 0 (WHY?)


‚ÄčIs this the DELTA section -- that is, the difference upon binding? If
yes, and you used a single-trajectory approach, then vdW and electrostatic
pairwise terms between *any* pair of residues that are both in the receptor
or both in the ligand should be 0. These energies are exactly pairwise
decomposable, so if the same pair is in both the bound and unbound states,
their contribution to binding will cancel exactly.

Looking at the data you pasted in your first email, it looks to me like ARG
220 is part of the ligand and both ASP 78 and GLU 74 are part of the
receptor (since their vdW and electrostatic pair contributions are *not*
zero upon binding).

However, GB is *not* pairwise decomposable, so you may have non-zero
contributions where the contributions from vdW and electrostatics are zero.

Also, I want to correct a rather embarrassing mistake in my last email --
GB *does* have a self-energy term, and that would also contribute to the
polar solvation term of a residue interacting with itself. However, the
self-pair energies for each residue *do* also include contributions between
pairs of atoms within that residue.

HTH,
Jason

-- 
Jason M. Swails
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Received on Thu May 05 2016 - 06:30:03 PDT
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