Subject: Re: CCL:REQUEST FOR AMBER PARAMETERS

From: [email-masked] (David Case)
Date: Fri, 27 May 94 09:44:17 PDT

There have been a number of requests recently for "AMBER" parameters
for various types of organic functionalities.  It's probably worthwhile
to keep the nomenclature straight:  AMBER is a suite of programs,
developed at UCSF and Scripps Research Institute, that allow certain
types of molecular mechanics calculations to be carried out.  People
use the AMBER programs with a number of force fields, including
AMBER/OPLS and CHARMM22, as well as the "default" force field that
comes with the code.

By common usage, the "AMBER" force field means the default force field
in that program, which is described in JACS 106:765 (1984) and J.
Comput. Chem.  7:230 (1986).  Strictly speaking, this covers only
proteins and nucleic acids, so that AMBER parameters for many
functionalities do not exist.

But we don't need to be too strict in our speaking, and we encourage
people to use the AMBER programs for lots of molecules.  Force fields
for many interesting molecules can be constructed from "obvious"
combinations of functional groups present in protein side chains.  The
new version of the force field (due to be released "soon") will cover a
much wider range of functionalities, and will include a general
"prescription" for extending it to new systems.  Of course, users will
have to evaluate the quality and robustness of these extensions....in
general, it is no simple matter to derive force fields for arbitrary
functional groups.

People who have generated AMBER compatible files for other things (sugars,
ethers, co-factors, etc.) might want to consider making them available for
other users.  You could send e-mail to me about what's available, and I
will publish a summary.

...dave case

=====================================================================
David A. Case                      |  internet: [email-masked]
Dept. of Molecular Biology, MB1    |  bitnet: case%scripps.edu@sdsc
The Scripps Research Institute     |  fax:   619-554-3789
10666 N. Torrey Pines Rd.          |  phone: 619-554-9768
La Jolla CA 92037  USA             |
=====================================================================