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
open your file and look for the error line I think it should be something
like
vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
do this before installing
tar jxvf Amber14.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
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
2016-02-23 12:39 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
> Hi everybody,
>
> I have Amber14, but when I use the command
>
> cpinutil.py -p crys.solv10.parm7 -igb 2 -o crys.solv10.cpin -op
> crys.solv10.modO.parm7 -resnames AS4 GL4 HIP
>
> I get this error:
>
> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy
> 1.9
> warnings.warn(_msg, ModuleDeprecationWarning)
> Traceback (most recent call last):
> File "/home/elisa/amber14/bin/cpinutil.py", line 289, in <module>
> main(opt)
> File "/home/elisa/amber14/bin/cpinutil.py", line 256, in main
> changeradii(parm, 'mbondi2').execute()
> NameError: global name 'changeradii' is not defined
>
> and OC crys.solv10.modO.parm7 is not produced. What's happening?
>
> Elisa
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 23 2016 - 19:30:04 PST
