...Hi
I had a similar problem in python2.7 respectively scripts for
MCPB.py and parmed.py
managed to solve AmberTools15 reinstalling as follows:
First installed libraries missing:
http://www.scipy.org/install.html
*sudo apt-get install python-numpy python-scipy python-matplotlib ipython
ipython-notebook python-pandas python-SymPy python-nose*
do this before installing
tar jxvf Amber15.tar.bz2
export AMBERHOME=`pwd`
*./configure --with-python /usr/bin/python2.7*
source amber.sh
make install
make test
The following command to install in parallel (requires first install mpi
with the same compiler gnu)
*./configure --with-python /usr/bin/python2.7 -mpi gnu*
make install
then it was just to set the bash file contents amber.sh
In my case:
export AMBERHOME="/home/marcelo/PROGRAMS/AMBER-NEW/amber14"
export PATH="${AMBERHOME}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
else
export
PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
fi
The problem in my case it was because they lacked python files and to set
needed which seek python2.7
...
Best regards
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 9:37 GMT-03:00 anu chandra <anu80125.gmail.com>:
> 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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>
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Received on Thu Mar 10 2016 - 05:00:06 PST
