Re: [AMBER] MMGBSA decomposition analysis

From: George Tzotzos <>
Date: Fri, 11 Nov 2016 22:30:46 +0100

Thank your for the prompt clarification.


> On 11 Nov 2016, at 22:27, Carlos Simmerling <> wrote:
> 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 <> 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 mailing list

AMBER mailing list
Received on Fri Nov 11 2016 - 14:00:02 PST
Custom Search