Re: AMBER: Poisson Boltzmann dynamics error

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From: Ray Luo <rluo.uci.edu>
Date: Tue, 08 Feb 2005 04:13:58 -0800

Rachel Burdge wrote:

>I am trying to run MD of a 53,059 atom system with a restraint on part
>of the protein. I solvated using a cap around the area of interest, and
>tried to run MD using igb = 10, which calculates a reaction field for
>the system, and the run crashes. Alternatively, this same system works
>fine with Generalized Born (igb = 1).
>
Hi Rachel,

I'm not sure I understand what you want to do. Are you trying to solvate
only a small portion of your protein with cap water in PBMD? As
described in the manual PBMD is only supported by developers when the
protein if fully solvated in cap water.

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 Thu Feb 10 2005 - 18:53:00 PST