AMBER Archive (2004)

Subject: Re: AMBER: how to use prep file

From: David A. Case (
Date: Mon Feb 23 2004 - 14:19:30 CST

On Mon, Feb 23, 2004, Fang, Jianwen wrote:
> I have a naive question. How should I use prep and frcmod files which I
> download from amber parameter database, to generate prmtop and prmcrd
> files for a cofactor I have pdb file. Do I need to modify atom types in
> my pdb file? Also how to construct a larger system which has this
> cofactor?

The "streptavidin/biotin" tutorial, at the Amber web site, shows how to
prepare small molecule (biotin) and one way to simulation its complex
with a protein (streptavidin).

...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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to