oops,
amber.python -c "import matplotlib; print(matplotlib)"
On Tue, Sep 12, 2017 at 10:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> yeah, just read my previous post about missing matplotlib.
>
> how's about
>
> python -c "import matplotlib; print(matplotlib)"
>
> On Tue, Sep 12, 2017 at 10:45 PM, jacky zhao <jackyzhao010.gmail.com>
> wrote:
>
>> Thanks for your help. I have reinstalled and rerun amber.python
>> $AMBERHOME/bin/mdout_analyzer.py as you suggested.
>> The error messages still can be observed.
>>
>>
>>
>> 2017-09-13 10:39 GMT+08:00 Hai Nguyen <nhai.qn.gmail.com>:
>>
>> > it's in
>> >
>> > $AMBERHOME/AmberTools/src/etc
>> > Do
>> >
>> > cd $AMBERHOME/AmberTools/src/etc && make
>> >
>> > will reinstall the original script to $AMBERHOME/bin
>> >
>> > Hai
>> > On Tue, Sep 12, 2017 at 10:36 PM, jacky zhao <jackyzhao010.gmail.com>
>> > wrote:
>> >
>> > > =.=! I have not backup the original mdout_analyzer.py. Could you
>> provide
>> > > it? thanks a lot
>> > >
>> > > 2017-09-13 10:18 GMT+08:00 Hai Nguyen <nhai.qn.gmail.com>:
>> > >
>> > > > 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/pyt
>> hon2.7/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
>> > > > >>
>> > > > >>
>> > > > >
>> > > > _______________________________________________
>> > > > 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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Received on Tue Sep 12 2017 - 20:00:07 PDT
