Re: [AMBER] MM-PBSA quasi harmonic

From: Jason Swails <>
Date: Sun, 1 Nov 2015 06:04:07 -0500

On Sat, Oct 31, 2015 at 11:32 PM, Debodyuti Dutta <
> wrote:

> Dear Amber users,
> During MM-PBSA analysis if in the input file, "entropy = 1" is used, then
> the program prints two
> types of binding energies.
> The first one is without consideration of entropy and
> the second one considering entropy (with quasi harmonic approximation).
> But during the residue decomposition, it only considers the value of
> delta-G obtained WITHOUT consideration of entropy.

‚ÄčNeither the GB nor the PB potential energy functions formally have a
pairwise decomposable functional form, which means that such decomposition
is not really correct. However, it is relatively straightforward to
*approximately* decompose the energy contributions into a per-residue, or
per-pairwise-residue form. This can lend qualitative understanding of
certain interactions, but keep in mind that neither GB nor PB are formally
decomposable in this manner.

On the other hand, entropy approximations are calculated from global
motions spread out over the entire complex‚Äč. Every residue contributes to
each vibrational "mode", and there is no straightforward way to even
approximately decompose the entropy (either quasi-harmonic or harmonic)
into per-residue contributions. So no attempt is even made.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 01 2015 - 03:30:04 PST
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