Hello,
If you are using mm_pbsa.pl, edit the file mm_pbsa_createinput.pm in
$AMBERHOME/src/mm_pbsa around lines 590-600 and add fillratio to the pbsa
input file.
If you are using MMPBSA.py, you may specify it right in the mmpbsa input
file in the &pb namelist.
Good luck!
Jason
2010/4/17 pxq <pangxueqintea.yahoo.com.cn>
> Hello everyone,
>
> When running mmpbsa I get the error:
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
> and stopped.
>
> Ray has suggested changing fillratio in the list, but where to change it?
>
> What is more, I have done mmpbsa calculation for this same system and the
> difference is that I changed some charge parameter for part of the receptor
> (which is not protein, and the new charge is come form a reference ). And
> then mmpbsa calculation stops at the same step when doing ligand related
> calculation (both receptor and complex related calculations are passed)
>
> And the memory of my computer is 24G, so is it possible of laking of
> memory?
>
> So do you have any suggestions?
>
> Thanks so much
>
> Best wishes
>
> Xueqin
>
>
>
> =========================================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379352 Fax: 0411-84675584
>
> ========================================================================================================================================
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Apr 17 2010 - 08:00:02 PDT
