Hi, Jason
Does this mean that MdoutAnalyzer.py works with Ubuntu but not with Fedora?
Yes, in my case, now it's works on Unbuntu13.04, centos6, it's not works on
Fedora which is run on VirtualBox, but it is works on another Fedora which
run on VMwarePlayer.
The Fedora platform is use a same virtual disk copy, the virtual disk is
created by VMwarePlayer, and the format is Virtual Machine Disk Format
(Fedora19-64.vmdk). VirtualBox can load it and run.
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:
> cd $AMBERHOME
> ./update_amber --apply mdoutanalyzer.patch
> make -c AmberTools/src/etc/ python
After I did it used your method, now it can works normally at Fedora which
running on VirtualBox use .vmdk virtual disk.
Thanks for your work.
Jacky
On Thu, Oct 3, 2013 at 11:36 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Oct 3, 2013 at 2:41 AM, Biao Ma <jackyma1981.gmail.com> wrote:
>
> > Hi, amberusers.
> >
> > I install the AmberTools13 on my Linux PC(Fedora19 and Ubuntu13.04).
> > On Ubuntu that's no Problem, but on Fedora, when I use the
> > MdoutAnalysizer.py to analysis the mdout file, I got some error:
> >
> > [mabiao.localhost amber12]$ MdoutAnalyzer.py
> > ~/Dropbox/workspace/amberMD/2013_run/1ag2_cphmd/1ag2.min.mdout
> > Traceback (most recent call last):
> > File "/home/mabiao/bin/amber12/bin/MdoutAnalyzer.py", line 8, in
> <module>
> > from mdoutanalyzer.graphproperties import GraphControlWindow
> > File "/home/mabiao/bin/amber12/bin/mdoutanalyzer/graphproperties.py",
> > line 6, in <module>
> > from mdoutanalyzer.widgets import LabeledEntry
> > File "/home/mabiao/bin/amber12/bin/mdoutanalyzer/widgets.py", line 7,
> in
> > <module>
> > import matplotlib.pyplot as plt
> > File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line
> 97,
> > in <module>
> > _backend_mod, new_figure_manager, draw_if_interactive, _show =
> > pylab_setup()
> > File
> > "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py",
> 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/MdoutAnalyzer.py", 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:
>
> cd $AMBERHOME
> ./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
> update.
>
> Thanks for the report!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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>
>
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Received on Thu Oct 03 2013 - 23:00:03 PDT
