Hi Elisa
u walk this way
vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
open the file and see the lines that the program shows 256 and 289
in my case I was missing libraries
show here a print of your file in this part for me to see and compare with my
installation
researching his error I found the following link
http://stackoverflow.com/questions/17557190/python-nameerror-global-name-is-not-defined
maybe you can help
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
2016-02-24 10:15 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
> Jason: I tried compiling Amber in serial, but I got exactly the same error.
>
> Marcelo: I did what you suggested, my amber.sh file looks exactly as yours,
> but I still have the same problem.
>
> Anyway I have this problem with cpinutil.py only using the -op flag;
> without it, it works.
>
> Other ideas?
> Elisa
>
> On Wed, Feb 24, 2016 at 4:26 AM, Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
>
> > 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Feb 24 2016 - 07:30:02 PST
