AMBER Archive (2005)

Subject: Re: AMBER: question about mmpbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Dec 12 2005 - 21:34:13 CST

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: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu