Re: Parameters for AMBER

From: David A. Case <>
Date: Fri 20 Sep 2002 06:53:18 -0700

On Thu, Sep 19, 2002, Kumpf, Bob wrote:

> I have visited the amber.ucsf web page and I found some links to parameter
> derivation efforts. However, I was wondering if you knew anything about the
> status of parameter derivation efforts for new/additional atom types for the
> AMBER force field. If so, which elements are under development? One
> element that shows up occasionally in protein modeling is Selenium (as part
> of the Selenomethionine analog of methionine). Do you, or anyone you know
> of, have any plans to tackle this element in the context of this residue?

Please send Amber related questions to the mailing list, not to me personally:
<>: that way many people can have a chance to see your
question. Maybe one of them will be familiar with work on selenium; I am

Most parameter development work for new functional groups, etc. is now
concentrated in the "antechamber" program and its associated data files.
There is also a (beginning) link to contributed force field parameters on
the Amber web site; we are hoping to encourage people to contribute things

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Fri Sep 20 2002 - 06:53:18 PDT
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