Re: [AMBER] MMPBSA error

From: Jason Swails <>
Date: Wed, 23 Dec 2015 13:09:59 -0500

On Wed, Dec 23, 2015 at 1:05 PM, Lara rajam <> wrote:

> Dear amber !
> I have went through the published papers , about single residue energy
> decomposition (SRED)
> I would like to know what exactly single residue energy decomposition(SRED)
> in amber ( MMPBSA), is per-residue contribution and single residue
> decomposition are both same.

​The way I would read this, per-residue decomposition and SRED are the same

> Is it possible to do both in PBSA and GBSA ,
> since the reported paper always says GBSA for SRED

​It is more straightforward based on the energy equations to decompose GB
into per-residue contributions than PB, I believe. GB is also a *lot*
faster to do decomposition analysis with. Since neither GB nor PB are
pairwise-decomposable, such decompositions really only have qualitatively
useful results, so there is not as much incentive to use PB.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 23 2015 - 10:30:04 PST
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