Re: [AMBER] The Error when I run

From: Jason Swails <>
Date: Thu, 3 Oct 2013 07:33:41 -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?

Does this mean that works with Ubuntu but not with Fedora?

> 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'

This is a strange error. It means one of two things: either the root
window has no geometry (which means it's not getting drawn) or your version
of Tkinter is, for some reason, giving a different format for the geometry
string which the regular expression does not match.

The window should be getting drawn (that's what the call to
root.update_idletasks() should be doing), and I would be surprised if the
format of the geometry string in Tkinter changed from one version to
another. I will try to reproduce the problem, but unless I can debugging
is going to be a challenge.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 03 2013 - 05:00:04 PDT
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