AMBER Archive (2006)

Subject: Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)

From: Ray Luo (rluo_at_uci.edu)
Date: Wed May 24 2006 - 18:14:33 CDT

Soo,

The paper is now in press in JPC-B, to appear in June, 2006. Since
ff03ua is very similar to ff03, please find out what GB parameters have
been used with ff03, for example, from Y. Duan's group. Maybe Dr. Yong
Duan can comment on this.

All the best,
Ray

Soonmin Jang wrote:

> Hi,
> I am trying to use the new united atom force field in amber9
> (leaprc.ff03ua) in combination with generalized Born solvation model.
> It seems the paper is not out yet but I wonder if I can use ff03ua
> with GB solvation. If so, what would be the "good" GB parameter for
> typical amino acid such as igb=1, 2, etc..?
> Also, can I use surface area correction here? (GBSA=1 option).
>
> Thank you.
>
> Soo
> 

-- 
====================================================
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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