It is unlikely that the complex topology file should have any water
molecules. The coordinates of the water molecules are probably stripped
when the snapshots are created.
-Jason
On Wed, Jun 16, 2010 at 10:13 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> Thank you so much. I just checked loading snapshot_com.crd.1 with
> complex.prmtop using vmd and the water molecules are all having abnormal
> bond lengths and the structure doesn't look good. I dont know what causes
> this problem but I will try the calculations from the beginning like making
> prmtop and inpcrd again, running MD and extracting snapshots again.
>
> 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
> _______________________________________________
> 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 Wed Jun 16 2010 - 19:30:04 PDT
