AMBER Archive (2004)

Subject: AMBER: Amber force field for protein-DNA system (again)

From: jz7_at_duke.edu
Date: Tue Jun 01 2004 - 14:51:59 CDT

Dear all,

First I apologize that I am so "new" to the Amber ff that I perhaps asked
the question not appropiatedly. After reading some related information
about Amber ff, I guess I could ask the question in another way.

I checked all the para*.dat files. Most of them are are both protein and
DNA (am I right?). But which one is the best for protein-DNA system?
Should I just use the latest parm99.dat. Also there is a question about
the parm99EP.dat (polarized ff with extra points). How does it work? What
kind of system or calculation is that for?

Thanks again!

Sincerely,
Jeny

On Tue, 1 Jun 2004 jz7_at_duke.edu wrote:

> Dear all,
>
> I am new to the Amber force field. I am wondering which parameter file I
> should use for a protein-DNA system? I saw parameters for protein and
> nucleic acid seperately. But is there a parameter file for both?
>
> Thanks a lot!
>
> Best,
> Jeny
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