Re: AMBER: Question about MMPBSA v9

From: Cenk Andac <>
Date: Wed, 11 Apr 2007 03:38:12 -0700 (PDT)

Dear Prof. Case and Holger,
  Thank you so much for the update. It is good to know more about the details of AMBER. From now onw I'll exclude Htrans/rot in my manuscripts.
  best regards,

"David A. Case" <> wrote:
  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?


        Date: Mon, 09 Apr 2007 15:58:09 +0200 From: To: "Cenk Andac" <> Subject: Re: Question about MM-PBSA v9
  Dear Jenk,

when thinking a bit more about whether H-trans./rot. should be
included, Dave Case concluded that it should _not_ be, for the
following reason:

In MM-PBSA, we compute only the potential energy parts of the binding
reaction, using the fact from classical statistics that the kinetic
energy parts must all cancel. The H-trans/rot. part then doesn't need
to be considered.

Best regards


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Received on Sun Apr 15 2007 - 06:07:04 PDT
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