oh but wait a second
your script is using python in /usr/bin/python (may be our mistake), which
is not what amber wants.
Can you try with the original mdout_analyzer.py (without your change):
amber.python $AMBERHOME/bin/mdout_analyzer.py
Hai
On Tue, Sep 12, 2017 at 10:10 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> ok, so try to
>
> - replace matplotlib.use("TkAgg") to "matplotlib.use("Agg")"
> - Delete any lines below the "except" you just deleted
>
> import os
>
> amberhome = os.getenv('AMBERHOME') or '$AMBERHOME'
>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
>
> 'you have sourced %s/amber.sh (if you are using
> sh/ksh/'
>
> 'bash/zsh) or %s/amber.csh (if you are using
> csh/tcsh)' %
>
> (amberhome, amberhome))
>
>
> I think that should work.
>
> Related? https://stackoverflow.com/questions/20582384/importerror-no-
> module-named-backend-tkagg
>
> Hai
>
> On Tue, Sep 12, 2017 at 9:52 PM, jacky zhao <jackyzhao010.gmail.com>
> wrote:
>
>> As your suggestion, I have remove try and except. The messages were
>> attached below:
>>
>>
>>
>>
>> Hai Nguyen <nhai.qn.gmail.com>于2017年9月12日 周二下午8:57写道：
>>
>> > So try to remove: "try" and "except" to see the real ImportError
>> > (Make sure to shift the line inside the try ... except to the left)
>> >
>> > Hai
>> >
>> > On Tue, Sep 12, 2017 at 8:54 AM jacky zhao <jackyzhao010.gmail.com>
>> wrote:
>> >
>> > > I have tried... Interesting...
>> > >
>> > > 2017-09-12 20:45 GMT+08:00 Hai Nguyen <nhai.qn.gmail.com>:
>> > >
>> > > > what happens if
>> > > >
>> > > > python $AMBERHOME/bin/mdout_analyzer.py
>> > > >
>> > > > If that work, should use that.
>> > > >
>> > > > Hai
>> > > >
>> > > > On Tue, Sep 12, 2017 at 8:39 AM, jacky zhao <jackyzhao010.gmail.com
>> >
>> > > > wrote:
>> > > >
>> > > > > Thanks a lot.
>> > > > > I have test all the modules mentioned in mdout_analyzer.py.
>> > Everything
>> > > is
>> > > > > OK... But I can not run mdout_analyzer.py for analyzing MD
>> results.
>> > > > >
>> > > > >
>> > > > >
>> > > > > 2017-09-12 20:25 GMT+08:00 Hai Nguyen <nhai.qn.gmail.com>:
>> > > > >
>> > > > > > hi,
>> > > > > >
>> > > > > > I think you're able to use that program and the original error
>> > > message
>> > > > is
>> > > > > > misleading.
>> > > > > > I don't know why then. Let's wait for Jason (wrote that
>> program) to
>> > > > reply
>> > > > > > to you.
>> > > > > >
>> > > > > > Hai
>> > > > > >
>> > > > > > On Tue, Sep 12, 2017 at 5:07 AM, jacky zhao <
>> > jackyzhao010.gmail.com>
>> > > > > > wrote:
>> > > > > >
>> > > > > > > Thank you for your immediately reply. I have installed
>> Amber16
>> > and
>> > > > > > > AmberTools17. When I was installed AmberTools17, python has
>> been
>> > > > > > suggested
>> > > > > > > to install. However, due to the limit of download speed. I
>> could
>> > > not
>> > > > > > > download and install python during AmberTools17 installation.
>> So
>> > I
>> > > > have
>> > > > > > > download python2.7.5 from the official website.
>> > > > > > > According to your suggestion, I have input these command
>> line. I
>> > > > > > > interestingly found there is no error message. These messages
>> > were
>> > > > > > attached
>> > > > > > > below:
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > > Hai Nguyen <nhai.qn.gmail.com>于2017年9月12日 周二下午12:39写道：
>> > > > > > >
>> > > > > > > > hi
>> > > > > > > >
>> > > > > > > > how did you install your python?
>> > > > > > > > can you try this:
>> > > > > > > >
>> > > > > > > > python -c "import mdoutanalyzer; print(mdoutanalyzer)"
>> > > > > > > >
>> > > > > > > > python -c "import os; print(os.getenv('PYTHONPATH'))"
>> > > > > > > >
>> > > > > > > > Hai
>> > > > > > > >
>> > > > > > > > On Tue, Sep 12, 2017 at 12:31 AM, jacky zhao <
>> > > > jackyzhao010.gmail.com
>> > > > > >
>> > > > > > > > wrote:
>> > > > > > > >
>> > > > > > > > > Hi everyone
>> > > > > > > > > When I used mdout_analyzer.py to analysis the output
>> files
>> > of
>> > > my
>> > > > > > > > > simulation, the error occur. According to the
>> suggestion, we
>> > > > have
>> > > > > > > source
>> > > > > > > > > the amber.sh without any error messages.
>> > > > > > > > > More importantly, I can use mmpbse.MPI.py to calculate
>> > binding
>> > > > > > energy
>> > > > > > > > > without any error.
>> > > > > > > > > The PYTHONPATH is
>> > > > > > > > > /home/jacky/amber16/lib/python2.7/site-packages:/home/
>> > > > > > > > > jacky/amber16/lib/python2.7/site-packages:/usr/lib64/
>> > > > > > > > > python2.7/site-packages/:/usr/
>> lib64/python2.7/site-packages/
>> > > > > > > > > :/home/jacky/amber16/lib64/python2.7/site-packages/
>> > > > > > > > >
>> > > > > > > > > Anyone can give me some suggestions?
>> > > > > > > > >
>> > > > > > > > > Thank you for taking your time
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > The error message was attached below:
>> > > > > > > > > analysis mdout_analyzer.py ../test22_md_1ms.out
>> > > > > > ../test22_md_1-1ms.out
>> > > > > > > > > ../test22_md_1-2ms.out ../test22_md_2ms.out
>> > > > > > > > > Traceback (most recent call last):
>> > > > > > > > > File "/home/jacky/amber16/bin/mdout_analyzer.py", line
>> 18,
>> > in
>> > > > > > > <module>
>> > > > > > > > > (amberhome, amberhome))
>> > > > > > > > > ImportError: Could not import Amber Python modules. Please
>> > make
>> > > > > sure
>> > > > > > > you
>> > > > > > > > > have sourced /home/jacky/amber16/amber.sh (if you are
>> using
>> > > > > > > > > sh/ksh/bash/zsh) or /home/jacky/amber16/amber.csh (if you
>> are
>> > > > using
>> > > > > > > > > csh/tcsh)
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > --
>> > > > > > > > > Lei Zhao, Ph.D.
>> > > > > > > > > International Joint Cancer Institute of the Second
>> Military
>> > > > Medical
>> > > > > > > > > University
>> > > > > > > > > National Engineering Research Center for Antibody Medicine
>> > > > > > > > > New Library Building 11th floor,800 Xiang Yin Road
>> > > > > > > > > Shanghai 200433
>> > > > > > > > > P.R.China
>> > > > > > > > > _______________________________________________
>> > > > > > > > > AMBER mailing list
>> > > > > > > > > AMBER.ambermd.org
>> > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > > > > >
>> > > > > > > > _______________________________________________
>> > > > > > > > AMBER mailing list
>> > > > > > > > AMBER.ambermd.org
>> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > > > >
>> > > > > > > --
>> > > > > > > Lei Zhao, Ph.D.
>> > > > > > > International Joint Cancer Institute of the Second Military
>> > Medical
>> > > > > > > University
>> > > > > > > National Engineering Research Center for Antibody Medicine
>> > > > > > > New Library Building 11th floor,800 Xiang Yin Road
>> > > > > > > Shanghai 200433
>> > > > > > > P.R.China
>> > > > > > >
>> > > > > > > _______________________________________________
>> > > > > > > AMBER mailing list
>> > > > > > > AMBER.ambermd.org
>> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > > >
>> > > > > > >
>> > > > > > _______________________________________________
>> > > > > > AMBER mailing list
>> > > > > > AMBER.ambermd.org
>> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Lei Zhao, Ph.D.
>> > > > > International Joint Cancer Institute of the Second Military
>> Medical
>> > > > > University
>> > > > > National Engineering Research Center for Antibody Medicine
>> > > > > New Library Building 11th floor,800 Xiang Yin Road
>> > > > > Shanghai 200433
>> > > > > P.R.China
>> > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Lei Zhao, Ph.D.
>> > > International Joint Cancer Institute of the Second Military Medical
>> > > University
>> > > National Engineering Research Center for Antibody Medicine
>> > > New Library Building 11th floor,800 Xiang Yin Road
>> > > Shanghai 200433
>> > > P.R.China
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> --
>> Lei Zhao, Ph.D.
>> International Joint Cancer Institute of the Second Military Medical
>> University
>> National Engineering Research Center for Antibody Medicine
>> New Library Building 11th floor,800 Xiang Yin Road
>> Shanghai 200433
>> P.R.China
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 12 2017 - 19:30:03 PDT
