Dear All
Thanks first for Marcelo and Hai for their support.
Replacing OS is an impossible option in case of using high-performance
computer. As well, installation of further python versions may result in
deep technical issues related to other software.
The problem of python2.6 with openmm package in AMBER14 would be solved by
replacing the headline of reporters.py file with
from __future__ import with_statement
In our case, this solution works well and the test stage was passed
successfully.
So, we believe reporters.py should be updated in the source files of
AMBER14.
Sincerely;
M. Ibrahim
On 30 October 2015 at 21:06, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> Hi,
>
> install Ubuntu on your machine.
>
> It is best suited for python.
>
> There tutorial link these facilities:
>
> Follow this first to install MPI for ubuntu.
>
>
> http://lsi.ugr.es/~jmantas/pdp/ayuda/datos/instalaciones/Install_OpenMPI_en.pdf
>
> http://jswails.wikidot.com/installing-amber14-and-ambertools14
>
> 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
>
> 2015-10-30 16:40 GMT-02:00 Mahmoud A. A. Ibrahim <m.ibrahim.compchem.net>:
>
> > Dear AMBER users
> > Very recently, we have purchased AMBER14. I downloaded it and followed
> all
> > instructions given in the manual to install AMBER14 on CentOS release
> 6.5 .
> > During testing AMBER14 serial version, we got the following
> python-related
> > error:
> > --------------
> > make test
> > (cd AmberTools/test && make test)
> > make[1]: Entering directory `/export/apps/amber14/AmberTools/test'
> > ./test_at_serial.sh
> >
> >
> /export/apps/amber14/lib/python2.6/site-packages/chemistry/openmm/reporters.py:743:
> > Warning: 'with' will become a reserved keyword in Python 2.6
> > Traceback (most recent call last):
> > File "<stdin>", line 18, in <module>
> > File
> > "/export/apps/amber14/lib/python2.6/site-packages/chemistry/__init__.py",
> > line 22, in <module>
> > from chemistry import openmm
> > File
> >
> >
> "/export/apps/amber14/lib/python2.6/site-packages/chemistry/openmm/__init__.py",
> > line 5, in <module>
> > from chemistry.openmm.reporters import (
> > File
> >
> >
> "/export/apps/amber14/lib/python2.6/site-packages/chemistry/openmm/reporters.py",
> > line 743
> > with open(self.fname, 'w') as f:
> > ^
> > SyntaxError: invalid syntax
> > make[1]: *** [test] Error 1
> > make[1]: Leaving directory `/export/apps/amber14/AmberTools/test'
> > make: *** [test.serial] Error 2
> > ----------------------------------------
> >
> > Our python version is:
> > Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
> > Is there a problem in using python2.6 with AMBER?
> > Any kind of support will be highly appreciated.
> > Thanks in advance
> > Sincerely;
> > M. Ibrahim
> >
> > --
> > Mahmoud A. A. Ibrahim
> > Head of CompChem Lab, Chemistry Department,
> > Faculty of Science, Minia University, Minia 61519, Egypt.
> > Email: m.ibrahim.compchem.net
> > m.ibrahim.mu.edu.eg
> > Website: www.compchem.net
> > _______________________________________________
> > 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
>
--
Mahmoud A. A. Ibrahim
Head of CompChem Lab, Chemistry Department,
Faculty of Science, Minia University, Minia 61519, Egypt.
Email: m.ibrahim.compchem.net
m.ibrahim.mu.edu.eg
Website: www.compchem.net
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Received on Sat Oct 31 2015 - 00:30:04 PDT
