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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Received on Thu Mar 10 2016 - 10:00:06 PST
