AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Fri Apr 14 2006 - 16:07:20 CDT

Thanks a lot Ray!
I set radiopt=0 and now I am getting the error message in the output file
as: PB bomb in pb_reslist(): maxnbr too small.
As this is related with the use of the pbsa program, I think the problem in
the calculation using Delphi is with Delphi. Meantime I tried to do the
calculation using just one monomer and I had no problems either using the
pbsa program either using the Delphi program. So, perhaps the problem may be
that Delphi is able to accept only a certain maximum number of atoms…
Could you please give me your opinion about this? Do you have any experience
of using mm_pbsa on large systems? Do you have any other idea about what may
be wrong with the calculation using Delphi?
Any suggestion would be very helpful.

Best regards
Tetrass

>From: "Ray Luo" <rluo_at_uci.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: MM-PBSA problem
>Date: Fri, 14 Apr 2006 09:57:52 -0700
>
>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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