What about the STDOUT and STDERR files? There is no information in the files
that you provided to help pinpoint what exactly is going wrong here, but
there must be some sort of warning or error message that got printed some
where, I assume. Another suggestion I might make is to try using MMPBSA.py (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/) instead of
mm_pbsa.pl. It might provide a more helpful error message.
-Bill
On Sat, Mar 12, 2011 at 12:58 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Hi Bill,
> I again tried to do the analysis and the output in logfile and again the
> same thing is happening. I am not able to figure out any error in the
> output
> file. Here I am attaching the files for your reference.
>
> Hirdesh
>
> On Fri, Mar 11, 2011 at 8:14 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > Obviously there is no error in the logfile. Have you checked all the
> other
> > output files for errors? Based on the logfile, it doesn't look like it
> > finished calculating the very last step for the ligand. Could the
> > calculation have ran out of time on the wall-clock?
> >
> > -Bill
> >
> > On Fri, Mar 11, 2011 at 9:24 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> > >wrote:
> >
> > > Hi All,
> > > I tried to calculate the binding free energy for my protein-ligand
> > complex.
> > > For the same I followed the tutorial given at amber site. The
> extraction
> > of
> > > coordinates was ok, and then I run the binding_energy.mmpbsa. The run
> was
> > > fine (as no error in the log file). It calculated the contribution of
> > > complex, receptor and ligand ( as displayed in the log file). Here I am
> > > attaching the log file as well. But at last I am not getting *
> > > snapshot_statistics.out*.
> > >
> > > I am not able to figure out the problem. Suggest me something
> > >
> > > Hirdesh
> > >
> > > _______________________________________________
> > > 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
> >
>
> _______________________________________________
> 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 Sat Mar 12 2011 - 04:30:02 PST
