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
> > > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 22 2011 - 07:00:04 PST
