Re: AMBER: mm_pbsa

From: Ray Luo <rluo.uci.edu>
Date: Thu, 18 Aug 2005 14:43:51 -0700

Amit,

You can find almost identical questions and answers on the Amber mailing
list archive. Also, please patch all reported bug fixes for pbsa and
recompile.

Best,
Ray

amit.mbu.iisc.ernet.in wrote:

>Dear Amber users,
>When I ran mm_pbsa.pl in amber8 , for my own molecular files some errors
>occur as follow,
>
>amber8/exe/pbsa -O -i pbsa.in -o pbsa_com.1.out -c 1pfy_com.crd.1 -p
>parm_com.top not successful
>
>It seems to be something wrong with pbsa. In pbsa_com.1.out:
>
> ======== PB Initialization ========
>
> Max PBMD Nonbonded Pairs: 4010779 2117502
>
> PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom
>
>
> Do you have any idea?
>
>Thanks in advance.
>
>amit
>
>
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-- 
====================================================
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 Aug 18 2005 - 22:53:01 PDT
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