> On Mar 11, 2016, at 7:03 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
>
> 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?
Yes. These warnings should be fixed in the next release.
HTH,
Jason
> 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
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>>>> 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 - 09:30:03 PST
