Re: AMBER: question about mmpbsa

From: Ray Luo <>
Date: Mon, 12 Dec 2005 19:34:13 -0800

Please use "radiopt=0" for your job. You can find out related info in
the Amber8 manual.

cui wei wrote:

> I run mm_pbsa after md ,but it failed, the output tell me that pbsa
> not successsful. and the out file side that
> ======== PB Initialization ========
> Max PBMD Nonbonded Pairs: 2228620 1176605
> PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom
> some one told me that means there are something wring with my
> molecular, i lose a sigma bond between tow heavy atom.
> but in fact i have finished a MD modeling allready
> my question is what is PB bomb?
> what's wrong with my MM_PBSA and how to fix it ?

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:
Home page:
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Received on Tue Dec 13 2005 - 13:53:01 PST
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