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
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 17 2011 - 09:00:02 PST
