AMBER Archive (2005)

Subject: Re: AMBER: The error during calculating PB with pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Sun Dec 04 2005 - 20:16:09 CST

Please search the Amber mailing list for answers of the following situation.

Ray

zhli_2000_at_126.com wrote:

>
> Dear all,
> When calculating the PB with pbsa, the error message is given in the
> ligand outfile (pbsa_lig.1.out) as following:
>
> ======== Setting up Grid Parameters ========
> Using bounding box for grid setup
> Bounding Box Center: 31.164 48.892 40.586
> Xmin, Xmax, Xmax-Xmin: 25.292 37.036 11.744
> Ymin, Ymax, Ymax-Ymin: 42.157 55.627 13.470
> Zmin, Zmax, Zmax-Zmin: 36.134 45.039 8.905
> beginning box center at level 1 31.164 48.892 40.586
> beginning box center at level 2 31.164 48.892 40.586
> Grid dimension at level 1 7 9 5
> Grid origin corrected at level 1 15.164 28.892 28.586
> Grid dimension at level 2 39 43 35
> Grid origin corrected at level 2 21.164 37.892 31.586
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
> I use the VMD to load the ligand, the first three structures of this
> ligand are good. So I don't know how to deal with this problem.
> Please give me some advices. Thanks a lot!
>
>
>
>
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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_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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