OK, I found out what is wrong. I don't know why this wasn't reported
before... Modify $AMBERHOME/AmberTools/src/etc/cpinutil.py and change the
string "changeradii" to "changeRadii" (notice the capital R). Then
recompile.
Thanks for the report, and sorry it took so long to fix.
HTH,
Jason
On Thu, Feb 25, 2016 at 1:33 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Sorry, I wasn't clear, "you" means the Amber Organization (after the
> payment of My university :D)!
>
> Elisa
>
> ----- Messaggio originale -----
> Da: "Jason Swails" <jason.swails.gmail.com>
> Inviato: 25/02/2016 03:28
> A: "AMBER Mailing List" <amber.ambermd.org>
> Oggetto: Re: [AMBER] R: Fwd: cpinutil.py problem
>
> 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
> > >>> _______________________________________________
> > >>> 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
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2016 - 16:00:06 PST
