Hi Jason,
Thank you for these background informations. I installed python2.7 and
tried the MMPBSA.py again and still got the same error. Maybe it could
help to re-install the MMPBSA.py stuff?I'm using Amber11 so MMPBSA.py
is installed by default but maybe this went wrong.
Quoting Jason Swails <jason.swails.gmail.com>:
> Hello,
>
> Python 3.0 is basically a re-design of the python language. As
> such, code
> written in python2.x cannot be directly run with python3.x
> interpreter.
> There are many websites that detail this.
> http://wiki.python.org/moin/Python2orPython3 is one of them. For
> MMPBSA.py,
> you need to use either python2.6 or python2.7 (though this is
> changing in
> the upcoming release). In order to get it to work for python3.x,
> you have
> to pass each module and program through the "2to3" utility. Type
> "which
> 2to3" to verify that you have this program.
>
> However, you have an error that pops up before this becomes an
> issue, I made
> a comment below.
>
> On Tue, Feb 22, 2011 at 9:26 AM, <poll.chemie.uni-hamburg.de>
> wrote:
>
> > 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
> >
>
> Just a little background to make this error make some sense: The
> first time
> a module is imported by python, the python interpreter "compiles"
> the module
> into what is called "byte-code", which is a binary .pyc file that
> loads
> faster than a text-based module. However, each version of python
> creates
> *different* byte-code binaries, so a .pyc file created with one
> version of
> python (i.e. python2.5) cannot be used with another version of
> python (i.e.
> python2.6, or python3.0, etc.). When you do try to import a .pyc
> file from
> a different version, it raises the exception you see (ImportError:
> Bad magic
> number). Try to find the default system python that compiled this
> version
> and use that (unless it's python < 2.6). The upcoming release will
> not be
> so finicky with regards to python version, and is a lot easier to
> install
> and run.
>
> Hope this helps,
> Jason
>
>
> > 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
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > > 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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> > 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 - 08:30:05 PST
