Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: Ray Luo <rluo.uci.edu>
Date: Wed, 30 Nov 2005 18:04:55 -0800

 

> Sorry! I forgot to mention that for PB calculation, I used readiopt =
> 1, not 0. For each radius, I changed Both Born radii of Mg2+ in prmpot
> file and corresponding Mg2+ radius in the mdread.f file (for sander
> and pbsa). Did I do something wrong?

Yes, you did it wrong. I suggest that you just use radiopt=0, i.e. use
the radii in the prmtop and change the radius of Mg2+ in the prmtop file.

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.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Fri Dec 02 2005 - 18:53:01 PST
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