Usually this high of a binding energy is indicative of an inconsistency
between the prmtop files and the coordinates in the generated snapshots. I
would suggest trying to visualize the snapshots with the prmtop files and
make sure those are consistent.
Good luck!
-Bill
On Wed, Jun 16, 2010 at 9:45 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> Hi all,
>
> I am running binding energy calculations using MMPBSA on amber 10.
> Previously I was getting some error messages which were solved when I used
> fillratio=4.0. Now I finished the calculation but the binding energy seems
> abnormally high. First I extracted 20 snapshots using the command
>
> $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
> then I run the command
>
> $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa_Example >
> extract_coords_Example.log
> I get a binding energy of -37091150.59 kcal/mol. (please see attached
> 20-snaps_statistics.out and other input and log files)
> Could somebody tell me what part of calculation I am possibly making
> mistake
> in ?
>
> Thank you
> Regards,
>
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> 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 Wed Jun 16 2010 - 19:00:05 PDT
