[AMBER] MMGBSA decomposition analysis

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 11 Nov 2016 22:16:41 +0100

My understanding is that per-residue decomposition analysis gives the contribution of each residue to the total DeltaG. In other words, the sum of all residue contributions equal total DeltaG.

I refer to the paper of B.R. Miller et al. (2012) which states that "decomposition analysis is not pairwise decomposable since the dielectric boundary defined between the protein and the bulk solvent is inherently non-local and depends on the arrangement of all atoms in spaceā€.

I take it this to mean that for a residue X the sum of its pairwise interaction energies IS NOT equal to the decomposition energy of the same residue? If this is true, what is the actual physical significance or pairwise energies other than being a measure of relative strength of residue-residue interactions.

I would be grateful if anyone could shed some light into this.


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Received on Fri Nov 11 2016 - 13:30:02 PST
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