It can happen! Thank you for your help! Now everything is working fine.
Elisa
On Fri, Feb 26, 2016 at 12:56 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> > > >> _______________________________________________
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> > >
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
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> > 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
>
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Received on Fri Feb 26 2016 - 02:00:03 PST
