AMBER Archive (2006)

Subject: Re: AMBER: PBSA calculation fail ....

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Oct 05 2006 - 11:36:32 CDT

Hi Changge,

Have you tried to reduce the scale to see whether it works. You are
using a grid spacing of 0.333 A (scale=3), which is very fine for a
system of 16,000 atoms.

Best,
Ray

Changge Ji wrote:

>hi, Folks.
>
>
>I did some MM_PBSA analysis with my dynamic traj.
>
> But it paused with the following error message : " PB Warning in epsbnd(): No neighbor found for boundary grids total: 61
> "
>
>parameters used in mm_pbsa.in are
>
>"
>PROC 2
>REFE 0
>INDI 1.0
>EXDI 80.0
>SCALE 3
>LINIT 3000
>PRBRAD 1.4
>"
>
>
>I found out that this error message comes from pb_exmol.f ,but I don't know what it really means ?
>
>And how can I fixed it .
>
>By the way ,my system is very large , the protein contains about 16000 atoms .
>but some parameters were already changed according to my protein ,(such as MAXMUM NUMBER OF ATOMS )
>
>
>
>
>
> Thank you very much for your sincerely help.
>
>
>　　　　　　　　
>Best wished ,
>
> Yours ,
>　　　　　　　　Changge Ji
>　　　　　　　　jcg_at_itcc.nju.edu.cn
>　　　　　　　　　　2006-10-05
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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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