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.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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Received on Tue Jun 01 2004 - 21:53:00 PDT
