AMBER Archive (2004)

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

From: jz7_at_duke.edu
Date: Wed Jun 02 2004 - 12:31:56 CDT

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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