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

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From: Ray Luo <rluo.uci.edu>
Date: Wed, 30 Nov 2005 20:31:29 -0800

The radii are assigned in routine "pb_aaradi()" in file "pb_init.f". You
can add a line there to assign radius for the ion and recompile. You can
set npbverb=1 to print out more information in the output file to check
your radii assignment.

mingche Pan wrote:

> Thank you, Ray! I guess that is the reason why all PB energies are the
> same. I will rerun the PB calculations. So when I used radiopt =1,
> where thoes parameters come from?
>

-- 
====================================================
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 - 21:53:01 PST