Date: Wed, 13 Sep 2017 10:45:30 +0800
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/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
> > > >>
> > > >>
> > > >
> > > _______________________________________________
> > > 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
(image/png attachment: _____________2017-09-13_______10.43.26.png)
