AMBER Archive (2005)

Subject: Re: AMBER: question about mmpbsa

From: cui wei (ethercui_at_gmail.com)
Date: Tue Dec 13 2005 - 19:09:29 CST

I had set radiopt=0 and try it again but the PBSA progress failed again
this time it was stoped during FDPB Summary
the output tell me that:

 PB Bomb in epsbnd(): No neighbor found for exposed boundary grid
34
          24 8

what is that mean?and how to fix it?
thanks

2005/12/13, Ray Luo <rluo_at_uci.edu>:
>
> 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/
> ====================================================
>
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