Dear Amber users,
While installing the latest MCPB program from
https://github.com/Amber-MD/pymsmt/releases following the steps in the
web-link, I experienced some errors as shown below.
1. The installation failed with following error,
$ sudo make install
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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Received on Thu Mar 10 2016 - 05:00:05 PST
