I have a general idea of what's going on, but not why it's happening or how
to fix it. I've never seen this error before.
On Thu, Nov 11, 2010 at 1:46 PM, Jemmy Hu <jemmyhu.sharcnet.ca> wrote:
> Hi Jason,
>
> Thank you for the python response.
> Any idea for the perl script mm_pbsa.pl, why does it ask for "$HTMLPATH"?
HTMLPATH is a variable set that has the location of online documentation
regarding mm_pbsa.pl, with forwards to frequently occurring issues people
may have. However, the issue is not that mm_pbsa.pl is looking for you to
input HTMLPATH or set it in some way, it's complaining that the Exporter in
mm_pbsa_global is failing to properly export HTMLPATH, which is set at the
bottom of that file.
My proficiency with perl stops at being able to see what a script is
*supposed* to do if it is syntactically correct (I don't know the syntax
well enough to correct it), so I can't say anything more than "
mm_pbsa_global.pm is trying to export HTMLPATH, but can't".
However, this online documentation is no longer available at the given link,
and it plays no part in the actual script execution, yet I don't know how to
render this error non-fatal. This may be a question you should ask to your
system administrator. There may be some system restriction/policy that
disallows whatever action it is that Exporter is trying. Someone with more
experience with Perl would most likely be able to provide a more helpful
response.
Hope this helps,
Jason
>
> Thanks,
> Jemmy
>
> >> Hello Everyone,
> >>
> >> We have some issues with mm-pbsa in Amber-11.
> >> When try to run mm-pbsa.pl in amber-11 on our Linux clusters, it gives:
> >>
> >> "$HTMLPATH" is not exported by the mm_pbsa_global module
> >>
> >> When try to run MMPBSA.py, it gives:
> >> Traceback (most recent call last):
> >> File "/opt/sharcnet/amber/11/bin/MMPBSA.py", line 44, in ?
> >> import inputparse, utils, alamdcrd # (2)
> >> ImportError: Bad magic number in /sharcnet/amber/11/bin/inputparse.pyc
> >>
> >>
> >
> > This means that the Python used to create the compiled python modules
> > (*.pyc) is different than the python that's trying to run them. Make
> sure
> > that when you are using the same Python version to install MMPBSA.py as
> you
> > are when you're trying to use it. Also note that Python version 2.6 or
> > greater is required to run MMPBSA.py.
> >
> > Good luck!
> > Jason
> >
> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Nov 11 2010 - 13:00:03 PST
