Subject: Re: CCL:More AMBER atom types

From: [email-masked] (Brad Isbister)
Date: Thu, 3 Nov 94 15:35:28 -0500

Charles Letner writes about the selection of atom types in AMBER.

The selection of atom types should always use a data set which resembles the
compounds to be investigated.  The original AMBER parameters which were
derived for proteins and nucleic acids are pretty good for the functional
groups found in such systems (peptide backbone, AA sidechains, C, T, G, A, etc).

If your system includes other functional groups, a literature search for AMBER
parameters which better reflect the 'real' system is a good idea.  These new
atom types can be included in an frcmod file for addition to the standard
parameter set.  Several papers have been written on 'non-standard' functional
groups.  In my work, I use the parameters for carbohydrates from S.W Homans,
Biochemistry, 1990, 29, 9110-9118.

If you want to know just what compounds were used to derive the standard AMBER
parameter set, get the original AMBER papers:  Kollman, Case, et al, JACS,
1984, 106, 765-784 and Kollman, Case, et al, J. Comp. Chem., 1986, 7, 230-252.
You should also look in the AMBER manual p23-24 for more info on the parameter
databases.

I've seen rumblings of "Does anyone(else) want to set up a database of
published AMBER parameters (or references to such)?"  But I don't think
anyone has taken the plunge and volunteered.

There is always the possibility that your compound is very different from
anything you can find.  In that case, refer to some papers on deriving atom,
bond, angle, and torsion parameters from spectroscopic data and/or Quantum
Mechanical simulation.  I haven't had to go that route yet.  Perhaps some
others on the CCL can help out with the references?

In the end, Molecular Mechanics is a game of assumptions.  Too many guesses and
your results are worthless or misleading; too few and you'll be running very
long and inefficient simulations.  You'll have to determine how similar the
database compounds are to the compound of interest.

Good Luck!

-Brad
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Brad Isbister					Duke University
[email-masked]				Department of Chemistry
Computational/Biophysical chemistry		E.J. Toone group