fantastic. Sorry for all the troubles you got.
cheers
Hai
On Tue, Sep 12, 2017 at 10:52 PM, jacky zhao <jackyzhao010.gmail.com> wrote:
> Hi everyone
> The problems have been solved by installation of matplotlib-tk.
> Thank you very much for Prof. Nguyen's valuable suggestions and kindly
> help.
>
> https://stackoverflow.com/questions/20582384/importerror-no-module-named-
> backend-tkagg
>
> 2017-09-13 10:45 GMT+08:00 jacky zhao <jackyzhao010.gmail.com>:
>
> > 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/ques
> >> tions/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/si
> >> te-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
> >
>
>
>
> --
> 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
Received on Tue Sep 12 2017 - 20:00:09 PDT
