Re: [AMBER] The Error when I run

From: Jason Swails <>
Date: Thu, 3 Oct 2013 10:36:21 -0400

On Thu, Oct 3, 2013 at 2:41 AM, Biao Ma <> wrote:

> Hi, amberusers.
> I install the AmberTools13 on my Linux PC(Fedora19 and Ubuntu13.04).
> On Ubuntu that's no Problem, but on Fedora, when I use the
> to analysis the mdout file, I got some error:
> [mabiao.localhost amber12]$
> ~/Dropbox/workspace/amberMD/2013_run/1ag2_cphmd/1ag2.min.mdout
> Traceback (most recent call last):
> File "/home/mabiao/bin/amber12/bin/", line 8, in <module>
> from mdoutanalyzer.graphproperties import GraphControlWindow
> File "/home/mabiao/bin/amber12/bin/mdoutanalyzer/",
> line 6, in <module>
> from mdoutanalyzer.widgets import LabeledEntry
> File "/home/mabiao/bin/amber12/bin/mdoutanalyzer/", line 7, in
> <module>
> import matplotlib.pyplot as plt
> File "/usr/lib64/python2.7/site-packages/matplotlib/", line 97,
> in <module>
> _backend_mod, new_figure_manager, draw_if_interactive, _show =
> pylab_setup()
> File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/", line
> 25, in pylab_setup
> globals(),locals(),[backend_name])
> I*mportError: No module named backend_tkagg*
> The above error is solved by installing *python-matplotlib-tk.*
> But got the next error, and cannot get some idea from Google.
> Could anyone can give me some help?
> Traceback (most recent call last):
> File "/home/mabiao/bin/amber12/bin/", line 59, in
> <module>
> rootgeo = [int(i) for i in geore.match(root.geometry()).groups()]
> AttributeError: 'NoneType' object has no attribute 'groups'

Scratch my last email. I think I found the problem. I installed Fedora on
a virtual machine and was able to reproduce the problem. The coordinate
system in Fedora can have negative values for some reason (the origin
placement is somewhat arbitrary in general), but the negatives were making
the regex fail to match.

A simple adjustment of the regex to allow for negative coordinates fixes
the problem for me. I've attached a patch that should fix your issues.
 After you download it, follow these steps and try again:

./update_amber --apply mdoutanalyzer.patch
make -c AmberTools/src/etc/ python

Please let me know if this fixes your problem so I can release this as an

Thanks for the report!

Jason M. Swails
Rutgers University
Postdoctoral Researcher

AMBER mailing list

Received on Thu Oct 03 2013 - 08:00:05 PDT
Custom Search