AMBER Archive (2007)Subject: Re: AMBER: Question about MMPBSA v9
From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 10 2007  21:20:58 CDT
On Mon, Apr 09, 2007, Cenk Andac wrote:
>
> I was wondering if it is really necessary to include Htrans/trot due to
> 6*translational/rotational degrees of freedom (1.79 kcal/mol at 300 K) in
> PBTOT values in MMPBSA 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?
...regards...dac

The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
