Subject: Comparison of force fields

From: Oliver Kohlbacher <[email-masked]>
Date: Thu, 15 May 1997 18:24:28 +0200

Dear Netters,

I'm trying to compare the total energies of different conformations of
large protein complexes (preferably in water).
The only obvious possibility to get these energies seems to be the use of
a molecular mechanics force field.
But there's quite a lot of different force field out there, most of them
are optimized (according to their authors) especially for proteins.
But there must be a difference! 
So, there's my question: Has anyone compared the quality of different 
force fields or has knowledge of recent publications concerning this 
problem?

Thank you
  Oliver Kohlbacher
-- 
----
 Oliver Kohlbacher   ([email-masked])
 Max-Planck-Institut fuer Informatik, Im Stadtwald, 66121 Saarbruecken
 Tel.: 0681-9325-505 Fax: 0681-9325-199

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From: Per-Ola Norrby <[email-masked]>
Date: Thu, 15 May 1997 19:53:28 +0200

>force fields or has knowledge of recent publications concerning this

	Dear Oliver,

	I was involved in a force field comparison a while ago, I believe
it's the most recent and general study of this kind, the references are:

Gundertofte, Liljefors, Norrby, Pettersson, J.Comp.Chem. 17, 429 (1996)
Gundertofte, Palm, Pettersson, Stamvik, J.Comp.Chem. 12, 200 (1991)

	I know that Marc Nicklaus did the same kind of study for charmm (in
press, I beleive), and Tom Halgren used a similar test set for MMFF in the
April 1996 issue of J.Comput.Chem.  However, these tests are for small
molecules.  I very much doubt that anybody has compared force fields
calculating on macromolecules.  Anyway, I believe there are much worse
sources of errors than the force field in this type of study, at least as
long as you stay with the dozen or so best protein force fields (Amber,
CFF, CharMM, MMFF, just to mention some).  My guess is that the solvation
model and the conformational sampling technique will be much more
important.  I don't know of any comparative study here, sorry.  I'd try a
continuum solvation model like GB/SA, just because it's rapid, and I don't
THINK anybody has shown it's generally inferior to explicit solvation.

	Regards,

	Per-Ola Norrby

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