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
Received on Tue Sep 12 2017 - 20:00:04 PDT
