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 - 05:30:03 PST
