Hi
as ubuntu linux use in notebook
to create files for AMBER
the amber.sh content in .profile
Best regards,
Marcelo
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-03-10 14:41 GMT-03:00 anu chandra <anu80125.gmail.com>:
> Hi,
>
> Thanks for the reply, Marcelo and Daniel.
>
> .Daniel, yes, I am trying to install it system-wide.
>
> . Marcelo, just to confirm it once again if I read your words correctly, do
> I have to reinstall the AmberTools to get rid off this?. Also, you
> suggested to copy the contents of amber.sh to .bashrc file in home
> directory, am I right?
>
>
> Many thanks
> Anu
>
>
> On Thu, Mar 10, 2016 at 4:16 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > On Thu, Mar 10, 2016 at 5:37 AM, anu chandra <anu80125.gmail.com> wrote:
> > > 1. The installation failed with following error,
> > >
> > > $ sudo make install
> >
> > Yikes - why are you using 'sudo' here? You should *not* have to use
> > 'sudo' to install Amber (unless I suppose you are trying to install a
> > system-wide version - is that what you are doing here?).
> >
> > -Dan
> >
> > > Makefile:1: /AmberTools/src/config.h: No such file or directory
> > > make: *** No rule to make target `/AmberTools/src/config.h'. Stop.
> > >
> > >
> > >
> > > Though I have the config.h file in /AmberTools/src/, the program failed
> > to
> > > detect it. I do have AMBERHOME set up in the .bashrc file and
> AmberTools
> > 15
> > > installed and successfully using it for quite some time.
> > >
> > > $ echo $AMBERHOME
> > > /usr/local/amber14
> > >
> > >
> > > I rectified this error by explicitly adding AMBERHOME path in the
> > Makefile
> > > in /usr/local/amber14/AmberTools/src/pymsmt/.
> > >
> > > 2. Afterwards, I faced the similar problem with 'make test' where 'make
> > > test' failed to look for MCPB.py though I set the AMBERHOME
> environment.
> > > Once again, I just overcome this error by explicitly adding AMBERHOME
> > path
> > > in the beginning of script 'Run.pymsmt' as follows,
> > >
> > > #!/bin/sh
> > >
> > > AMBERHOME=/usr/local/amber14
> > >
> > > . ../../program_error.sh
> > >
> > > dacdif=$AMBERHOME/AmberTools/test/dacdif
> > >
> > > 3. Unfortunately, 'make test' once again failed with a different error
> > as
> > > shown bellow, and I will be grateful if somebody can help me to figure
> > out
> > > the error here.
> > >
> > >
> > > *Traceback (most recent call last): File
> "/usr/local/amber14/bin/MCPB.*
> > >
> > > *py", line 26, in <module> from mcpb.gene_model_files import
> > > get_ms_resnames, gene_model_filesImportError: No module named
> > > mcpb.gene_model_files*
> > >
> > >
> > > I had a look at Amber mail list and tried different options, but
> failed.
> > >
> > > a). I do sourced amber.sh and also set it up in .bashrc file.
> > >
> > > b). echo $PYTHONPATH
> > >
> >
> /usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages:/usr/local/amber14/lib/python2.7/site-packages
> > >
> > > I do added PYTHONPATH in .bashrc also. But, I just wonder why
> > > echo $PYTHONPATH shows multiple paths!!. Is this causing the problem?
> If
> > > so, how to remove multiple paths?
> > >
> > > c). I do have file gene_model_files.py in
> > > $AMBERHOME/lib/pythonx.2.7/sitepackages/mcpb
> > >
> > > d). $ python -c "import scipy" did not show any error message
> > >
> > > e). $ python -c "import sys; print sys.path"
> > > ['', '/usr/lib/python2.7/site-packages/argparse-1.4.0-py2.7.egg',
> > > '/usr/lib/python2.7/site-packages/networkx-1.10-py2.7.egg',
> > >
> '/usr/lib/python2.7/site-packages/biopython-1.65-py2.7-linux-x86_64.egg',
> > > '/usr/lib/python2.7/site-packages/GridDataFormats-0.3.0-py2.7.egg',
> > >
> >
> '/usr/lib/python2.7/site-packages/MDAnalysis-0.11.0-py2.7-linux-x86_64.egg',
> > > '/usr/lib/python2.7/site-packages/pyPcazip-1.4.4-py2.7.egg',
> > > '/usr/lib/python2.7/site-packages/PROPKA-3.1-py2.7.egg', '
> > > */usr/local/amber14/lib/python2.7/site-packages*',
> > > '/usr/lib64/python27.zip', '/usr/lib64/python2.7',
> > > '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk',
> > > '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload',
> > > '/usr/lib64/python2.7/site-packages',
> > > '/usr/lib64/python2.7/site-packages/gtk-2.0',
> > > '/usr/lib/python2.7/site-packages']
> > >
> > >
> > > Any help would be highly appreciated
> > >
> > >
> > > Many thanks
> > > Anu
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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Received on Thu Mar 10 2016 - 11:00:07 PST
