I tried to use MMPBSA.py.As mentioned in the manual a python version
2.6 or later is needed. I used python3.0 which is already installed
on our machines. As I executed the MMPBSA.py I got the following
error:
python3.0 $AMBERHOME/bin/MMPBSA.py
Traceback (most recent call last):
File "/opt/amber11/bin/MMPBSA.py", line 44, in <module>
import inputparse, utils, alamdcrd # (2)
ImportError: Bad magic number in /opt/amber11/bin/inputparse.pyc
The script finds the inputparse.pyc but it seemed to be broken because
when I rename the inputparse.pyc I get
Traceback (most recent call last):
File "/opt/amber11/bin/MMPBSA.py", line 44, in <module>
import inputparse, utils, alamdcrd # (2)
ImportError: No module named inputparse
So the MMPBSA.py might not work with Python3.0?Any thoughts on this?
Thx in advance
Bernhard Poll
Quoting Jason Swails <jason.swails.gmail.com>:
> 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
>
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Received on Tue Feb 22 2011 - 06:30:05 PST
