Re: [AMBER] and issues in Amber-11

From: Jason Swails <>
Date: Thu, 11 Nov 2010 14:50:12 -0600

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 <> wrote:

> Hi Jason,
> Thank you for the python response.
> Any idea for the perl script, why does it ask for "$HTMLPATH"?

HTMLPATH is a variable set that has the location of online documentation
regarding, with forwards to frequently occurring issues people
may have. However, the issue is not that 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 " 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

Hope this helps,

> Thanks,
> Jemmy
> >> Hello Everyone,
> >>
> >> We have some issues with mm-pbsa in Amber-11.
> >> When try to run in amber-11 on our Linux clusters, it gives:
> >>
> >> "$HTMLPATH" is not exported by the mm_pbsa_global module
> >>
> >> When try to run, it gives:
> >> Traceback (most recent call last):
> >> File "/opt/sharcnet/amber/11/bin/", 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 as
> you
> > are when you're trying to use it. Also note that Python version 2.6 or
> > greater is required to run
> >
> > Good luck!
> > Jason
> >
> >
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Nov 11 2010 - 13:00:03 PST
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