Dear Dr. Bill,
Is there some rule like how many snapshots should be extracted for 2 ns of
simulation (my case for example=2 ns of production MD) ?
Is this inconsistency, the result of less number of snapshot. I also tried
with just one snapshot and 5 snapshots and binding energy in both cases was
-41kcal/mol (looks correct).
Thank you
Regards,
On Thu, Jun 17, 2010 at 10:49 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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,
> >
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Wed Jun 16 2010 - 19:00:08 PDT
