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
