Date: Tue, 12 Sep 2017 20:54:12 +0800
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
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(image/png attachment: _____________2017-09-12_______8.52.50.png)
