AMBER Archive (2005)

Subject: Re: AMBER: warning in PBSA

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Mar 23 2005 - 11:42:34 CST

Fabien,

Could you email me your input/data files so I can take a look?

Best,
Ray

Fabien Cailliez wrote:

> Dear all,
>
> I have problems when using PBSA program on my systems, when running
> MMPBSA analysis.
> I have a system of roughly 3300 atoms.
> The calculations ends but there is one warning in the outuput file :
> PB Warning in epsbnd(): No neighbor found for reentry boundary grid
> What does this warning mean ?
> The second problem is with a system with 6600 atoms.
> The calculation stops with an error message in the output :
> PB bomb in pb_saarc(): Allocation aborted
>
> I am working on a Linux machine with 2G of physical memory.
>
> The input file for PBSA is :
> File generated by mm_pbsa.pl. Using PB
> &cntrl
> ntf = 1, ntb = 0,
> igb = 10, dielc = 1.0,
> cut = 99999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 0, ntmin = 2,
> &end
> &pb
> epsin = 1.0, epsout = 78.5,
> istrng = 0, radiopt = 0,
> sprob = 1.4, space = 2,
> maxitn = 250
> npbverb= 1
> &end
>
> Thanks in advance for your answers,
> Fabien
> 

-- 
====================================================
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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