Did you recompile mm_pbsa.pl after making that addition?
Another suggestion would be to use MMPBSA.py from AmberTools 1.5. MMPBSA.py
has fillratio has an input variable that you can just put in the input file
instead of modifying the source code.
-Bill
On Tue, Oct 18, 2011 at 2:14 AM, Prajwal Nandekar <prajwal.pharm07.gmail.com
> wrote:
> Hi,
>
> i run mmpbsa calculation with amber10,
> i have successfully extracted the coordinates from mdcrd.
> but when i run script "binding_energy.mmpbsa" for calculation of its
> binding
> energy.
>
> The calculation stop with following error message:
>
> sander -O -i pbsa_lig.in -o pbsa_lig.89.out -c ./snapshot_lig.crd.89 -p
> ./raf.prmtp not successful
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
> then I searched for this error and i got result on link "
> http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html"
> then added the following line (#435) to $AMBERHOME/src/mm_pbsa/
> mm_pbsa_createinput.pm:
> print OUT " fillratio=3 \n";
>
> But still the error persist.
>
> What to do please help me.
>
> Thanking you
> --
> *Prajwal Nandekar
> Ph. D. Scholar
> Department of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
> Mob. 09780741228*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Oct 18 2011 - 04:30:03 PDT
