Re: AMBER: Question about MMPBSA v9

From: David A. Case <>
Date: Tue, 10 Apr 2007 19:20:58 -0700

On Mon, Apr 09, 2007, Cenk Andac wrote:
> I was wondering if it is really necessary to include H-trans/trot due to
> 6*translational/rotational degrees of freedom (1.79 kcal/mol at 300 K) in
> PBTOT values in MM-PBSA v9 computations?

No. If you are referring to Eq.2 in JCC 25:238 (2003), there is a mistake
there (I think). The Hrot/trans is a kinetic energy term, which will
cancel out on both sides of a balanced chemical reaction: in the classical
limit, there will always be exactly the same kinetic thermal energy on
both sides.

The mistake was caused by thinking about quantum energy formulas from normal
modes: there the energies include both kinetic and potential terms, so you
have to include all of the kinetic energy terms on both sides of the chemical
equation. But Hgas in the above paper is just a potential energy term
(viewed classically), so you don't want to add in a kinetic energy term
like Hrot/trans.

Clear as mud?


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Received on Wed Apr 11 2007 - 06:07:45 PDT
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