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
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> 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)
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Received on Thu Mar 10 2016 - 08:30:07 PST
