AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: amit_at_mbu.iisc.ernet.in
Date: Sat Aug 20 2005 - 02:46:24 CDT

Hi Ray,
      Thank you very much for your help. I would like to change the grid
size resolution to 0.65Angs. I have changed the SCALE parameter of
mm_pbsa.in file inorder to get the desired resolution.
 Some errors occur as follow,
PB bomb in pb_read(): cutfd must be <= cutsa

with regards,
amit

> Amit,
>
> You can find almost identical questions and answers on the Amber mailing
> list archive. Also, please patch all reported bug fixes for pbsa and
> recompile.
>
> Best,
> Ray
>
> amit_at_mbu.iisc.ernet.in wrote:
>
>>Dear Amber users,
>>When I ran mm_pbsa.pl in amber8 , for my own molecular files some errors
>>occur as follow,
>>
>>amber8/exe/pbsa -O -i pbsa.in -o pbsa_com.1.out -c 1pfy_com.crd.1 -p
>>parm_com.top not successful
>>
>>It seems to be something wrong with pbsa. In pbsa_com.1.out:
>>
>> ======== PB Initialization ========
>>
>> Max PBMD Nonbonded Pairs: 4010779 2117502
>>
>> PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom
>>
>>
>> Do you have any idea?
>>
>>Thanks in advance.
>>
>>amit
>>
>>
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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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