AMBER Archive (2005)

Subject: Re: AMBER: "personality" of Amber force field

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Mar 17 2005 - 16:17:03 CST

Hui-Hsu Tsai wrote:

>I tried beta-hairpin using amber ff99 + GB model. It forms helix quickly
>in conventional MD simulation at 325 K. I do not have this experience to
>observe helix formation so fast in CHARMM FF. Maybe I should use replica
>exchange MD to generate the decoy to examine the population of
>helix and beta secondary structures.
>
>Gavin
>
Professor Yong Duan probably should answer this. His ff03 has been shown
to fold beta hairpin without problem in GB. We also find it okay in PB.
Which GB are you using?

Best,
Ray 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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