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From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Fri, 11 Nov 2016 16:27:51 -0500

you're right that it isn't decomposable, because moving one atom can change

the effective radii of many atoms, and that changes all of their pairwise

interactions. I think the point of doing the decomposition is to assume

that the major change is in the direct interactions, and these are

accumulated pairwise. this assumes that the effective radii are constants,

at least in that structure. you get the information about the strength of

an interaction, including solvent screening, under the assumption that

nothing else changes. it can be very informative, but you're correct that

it is not rigorously correct and is more of a first order approximation.

On Fri, Nov 11, 2016 at 4:16 PM, George Tzotzos <gtzotzos.me.com> wrote:

*>
*

*> 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.
*

*>
*

*> Regards
*

*>
*

*> George
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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Received on Fri Nov 11 2016 - 13:30:03 PST

Date: Fri, 11 Nov 2016 16:27:51 -0500

you're right that it isn't decomposable, because moving one atom can change

the effective radii of many atoms, and that changes all of their pairwise

interactions. I think the point of doing the decomposition is to assume

that the major change is in the direct interactions, and these are

accumulated pairwise. this assumes that the effective radii are constants,

at least in that structure. you get the information about the strength of

an interaction, including solvent screening, under the assumption that

nothing else changes. it can be very informative, but you're correct that

it is not rigorously correct and is more of a first order approximation.

On Fri, Nov 11, 2016 at 4:16 PM, George Tzotzos <gtzotzos.me.com> wrote:

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Received on Fri Nov 11 2016 - 13:30:03 PST

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