By the way..this is the message I get now using cpinutil:
*elisa.agachon:~$ cpinutil.py -p 2rn2.parm7 -igb 2 -o 2rn2.cpin -op
2rn2.modO.parm7 -resname AS4 GL4 HIP CYS LYS
TYR/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)/home/elisa/amber14/lib/python2.7/site-packages/chemistry/amber/amberformat.py:31:
DeprecationWarning: writeParm has been deprecated, use write_parm instead
DeprecationWarning)CPIN generation complete!*
Is this normal?
Elisa
On Fri, Feb 26, 2016 at 10:59 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> 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
>> > > >> _______________________________________________
>> > > >> 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
>>
>
>
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Received on Fri Mar 11 2016 - 04:30:03 PST
