What tarball did you receive from me?
On Wed, Feb 24, 2016 at 1:18 PM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Hi Jason,
>
> The AmberTools15 I have has been downloaded from the amber website, and I
> received the amber14 tarball from you. I am not expert enough to play with
> github :)
>
> Tell me if you find something because I really need it.
>
> Thank you,
> Elisa
>
> ----- Messaggio originale -----
> Da: "Jason Swails" <jason.swails.gmail.com>
> Inviato: 24/02/2016 18:31
> A: "AMBER Mailing List" <amber.ambermd.org>
> Oggetto: Re: [AMBER] Fwd: cpinutil.py problem
>
>
>
> > On Feb 24, 2016, at 8:15 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
> >
> > 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?
>
> Have you perhaps installed a newer version of ParmEd from Github?
>
> The cpinutil script in AmberTools 15 only works with ParmEd from
> AmberTools 15. I'll try to dig up an AmberTools 15 release to see what
> might be causing this problem, but I don't think you should get this error
> if you are using just AmberTools 15 components... (And ParmEd from Github
> shouldn't leak into AmberTools 15 applications anyway since the package
> names were changed). So I'm really not sure how this is happening...
>
> > 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
> >>> _______________________________________________
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 24 2016 - 18:30:03 PST
