If you can access the latest PBSA in AMBERTOOLS 1.4, you won't need to
reset it. The program will reset it automatically.
However, if you're using Amber10 or earlier version, you'll need to
insert "fillratio = 3" into the mmpbsa perl script that writes the input
files for mmpbsa calculations. This has been mentioned on the list
several times.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
On 8/27/2010 2:20 AM, Asfa Ali wrote:
> Hi,
>
> While running mmpbsa.pl, the run is getting aborted. In the pbsa_lig.5.out,
> I found :
>
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
> I checked the mailing list and found that perhaps I have to change the
> fillratio from 2.000 to 3.000.
>
> But how to exactly do so? Where would I find the fillratio?
>
> Plz tell the detailed procedure.
>
> Thanks a lot..
> Asfa.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 27 2010 - 10:30:04 PDT
