AMBER Archive (2004)

Subject: Re: AMBER: how to use prep file

From: David A. Case (case_at_scripps.edu)
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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
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