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

From: <jz7.duke.edu>
Date: Wed, 2 Jun 2004 13:31:56 -0400 (EDT)

Sorry to post it again. But I am hoping that I could find some answers
here.

Here is my old post:

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

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Received on Wed Jun 02 2004 - 18:53:00 PDT
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