Perhaps try using MMPBSA.py (
http://ambermd.org/tutorials/advanced/tutorial3/py_script) instead. It may
print out a more helpful error message if there is, indeed, one.
Good luck,
Jason
On Thu, Feb 17, 2011 at 11:38 AM, <poll.chemie.uni-hamburg.de> wrote:
> When I run this by hand no error occures and nothing strange in the
> output-file. I tried to run the MMPBSA without this snapshot which
> didn't work as well.
>
> Quoting steinbrt.rci.rutgers.edu:
>
> > Hi,
> >
> > > /opt/amber11/bin/sander -O -i pbsa_com.in -o
> > pbsa_com.1.out -c
> > > ./snapshot_com.crd.1 -p ./1q3w_out.prmtop not successfu
> >
> > this is the actual command that failed. You could run it by hand
> > and see
> > what the output says. pbsa can sometimes crash on unusual, large
> > (or even
> > random?) conformations, often the output file will contain an
> > explanation
> > or a suggestion of what parameter to change.
> >
> > In the worst case, you could do the MMPBSA analysis without data
> > from that
> > one problematic snapshot.
> >
> > Thomas
> >
> > Dr. Thomas Steinbrecher
> > formerly at the
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 17 2011 - 09:30:05 PST
