AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA entropy question

From: David A. Case (
Date: Tue Oct 31 2006 - 19:04:29 CST

On Tue, Oct 31, 2006, Barbault Florent wrote:
> I have several questions about MMPBSA scientific background, maybe trivial,
> and especially the for the entropic effect. If I have correctly understood
> the method, the solute entropic effect is divided into four parameters :
> translation, rotation, vibration and configuration.
> In the MMPBSA tutorial I found that the configuration term is "the
> configurational entropy contribution from sidechain reorganization. Note that
> configurational entropy is neglected in this protocol, but may be
> significant." Why only sidechain?

A normal mode analysis just considers a single local minimum.
"Configurational" entropy is that arising from the fact that there are likely
to be multiple minima, adding to the "disorder" in the system. This is not
limited to sidechains, although their contribution is often the largest, since
there may be multiple rotamers that have significant populations.

> If you start with 3 trajectories (ligand,
> target and complex) this effect couldn't be overcome?

No. Of course, there may in practice be a good deal of cancellation of
configurational entropy between (say) the complex and the receptor, but nothing
guarantees this.

> The translation and rotation terms came directly from statistical mechanics.
> Therefore, why these values are only accessible with the normal mode option?

Just a quirk of how Amber was coded. As you point out, you could easily write
a routine to compute these values without having to do a normal mode analysis.
But since they were already computed and printed out as a part of normal modes,
we didn't write a second routine. Maybe this would be a good point for someone
to improve upon.

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