Subject: Re: CCL:Molecular Mechanics

From: "Robert K. Szilagyi" <[email-masked]>
Date: Wed, 22 Nov 1995 11:56:42 -0800

> >  The reason that I ask is that I obtained the following energies from
> > MM optimisations for complexes of the same ligand but with different
> > ions:

	My 0.02$ to this question is that molecular mechanical results MUST NOT
be compared with each other if the molecules are different. It has no chemical
and physical meaning at all! The MM model is constructed with different
equations due to the different parameters.

	The different molecules contain different atom types, different bond
types, thus represent different "sub force fields". Only when the non-valence
type interactions are compared (van der Waals, Coulomb, etc.) can be acceptable
in some cases and with heavy restrictions.

	I have successfully overcame this problem several times in case of
transition metal complexes using a higher level of theory (semi-empirical or ab
initio calculations) single point energy calculation. The absolute values of
energies are still uncorrect, but realive values seem to be fine!
Try it and let us know the results!

		Best wishes,

				Rob

-- 
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Robert K. Szilagyi                        University of Veszprem   METMOD FF
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               http://mm1.vein.hu/        http://mm2.vein.hu/~isom
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  *************** All opinions are my own, NOT my employer's ***************
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---

From: Charles Letner <[email-masked]>
Date: Fri, 24 Nov 1995 13:39:49 -0500 (EST)

> equations due to the different parameters.
	So the question that I always end up at is, what constitutes a 
different molecule?  Further, how to assess whether two molecules are 
"close enought."  For example, a organic molecule may have a chiral 
center.  So what about the two conformers?  I would say they are close 
enough to compare energies.  However, it is not diffiult to envison a 
case in which the non-bonded interactions between the two are not the 
same.  As a consequence, the two have different "equations."  For the 
biopolymer case, how about two calculations in which different amounts of 
solvent are added?  Though the biopolymer may be identical in the two 
systems the solvent will be different.  In this case the energy of the 
system will be different.  As a result, I expect that the energy of the 
biopolymer will be different.  I quess then the question of MD 
calculations to estimate free energy differences then begs to be asked 
- but I'll stay away from that.....  ;)
My $0.02 worth.
Chuck

Charles Letner
Wright State University
Department of Biochemistry
Dayton, OH 45435
e-mail: [email-masked]