AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Apr 14 2006 - 11:57:52 CDT

Well, I can point out why your second try with pbsa failed. You have to
use radiopt = 0 because you have used non-standard Amber atom types,
i.e. from antechamber.

Miguel Ferreira wrote:

>
> To see if the problem was with Delphi, I try to use the PB method
> implemented in the pbsa program, but it also gives error:
>
> -- > /scratch/programs/amber8/amber8_mod//exe/pbsa -O -i
> pbsa.in -o pbsa_com.1.out -c ./complexo-modelado_com.crd.1 -p
> ./complexo-finalsolv_oct_semsolv.top not successful
>
> [1] Exit 25 mm_pbsa.pl mm.exp2.in > mm.exp2.out
>
>
> The pbsa_com.1.out end with the following error:
>
> ======== PB Initialization ========
>
> Max PBMD Nonbonded Pairs: 7136003 3767472
>
> PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom
> 

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