The manual also metioned in page 27 that "some codes (like pytraj and
ParmEd) work unchanged in both Python 2.7 and Python 3.x, while *others
need to be converted using 2to3 upon installation*." This indicated that
python 2.7 and python 3.x are not compatibility well. MMPBSA.py belongs to
so-called "others" which need to be converted using 2to3 upon installation;
jing
On Wed, Jan 4, 2017 at 9:06 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Wed, Jan 4, 2017 at 1:43 PM, Huang Jing <jing.huang8911.gmail.com>
> wrote:
>
> > In amber 16 manual page 26, python 2.7 and later version is required and
> > the manual contains nothing about python 3;
> >
>
> Isn't Python 3 is later version (vs python 2.7)?
> I believe we explicitly mention about python 3.4 in "2.2.3. Supported
> Python versions" (page 27).
>
> The only reason amber use python2.7 as default because other packages
> having interface with amber such as phenix, pyrosetta, ... only works with
> py2.
>
>
> > From my knowledge, python 2 and python 3 are two different schemes
>
>
> Not very different. Python 3 changes some syntax (nicer) and add more
> (nice) stuff.
> http://python-future.org/compatible_idioms.html
>
> and they
> > developed separately,
>
>
>
> > athough some simply python scripts can run properly
> > both with python 2 and python 3;
> >
>
> ParmEd (https://github.com/Amber-MD/ParmEd), Pytraj (
> https://github.com/Amber-MD/pytraj),
> nglview (https://github.com/Amber-MD/nglview) are three examples of
> complicated projects in AMBER that can be run in both python 2 and python 3
> without changing anything.
> (of course, you need to use the same python version after compiling some C
> extensions)
>
> cheers
> Hai
>
> jing
> >
> > On Wed, Jan 4, 2017 at 8:25 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > On Wed, Jan 4, 2017 at 1:13 PM, Huang Jing <jing.huang8911.gmail.com>
> > > wrote:
> > >
> > > > Possibly your default python is python3 and the MMPBSA.py is written
> in
> > > > python2.if you have Python version 3, the utility 2to3 must be
> present
> > to
> > > > translate the code into Python 3 syntax;
> > > > Following is the details about MMPBSA.py script
> > > > http://ambermd.org/tutorials/advanced/tutorial3/py_script/
> > > > files/MMPBSA_Python_Manual.pdf
> > > > jing
> > > >
> > >
> > > all Python programs in AmberTools will work with both Python 2 and 3.
> > User
> > > needs not to use anything else to convert.
> > > You just need to recompile AmberTools.
> > > Please double-check the Python section in Amber 16 manual.
> > >
> > > Hai
> > >
> > >
> > > >
> > > > On Wed, Jan 4, 2017 at 8:00 PM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> > > >
> > > > > make distclean and recompile Amber/AmberTools will help.
> > > > >
> > > > > PS0: "not working" is not very helpful info.
> > > > > PS1: We've updated info for Mac OS here (much simpler):
> > > > > http://ambermd.org/ubuntu.html
> > > > > PS2: per Python version, I suggest you let AMBER install the
> > Miniconda
> > > > > distribution for you during installation process.
> > > > >
> > > > > .Dave: from the link: Mac OS on "ubuntu" link. Should we move?
> > > > > Hai
> > > > >
> > > > > On Wed, Jan 4, 2017 at 12:54 PM, erik rp zuiderweg <
> > zuiderwe.umich.edu
> > > >
> > > > > wrote:
> > > > >
> > > > > > My older MMPBSA calculations are not working any more, likely
> due
> > to
> > > > my
> > > > > > OS “up”grade.
> > > > > > Can anyone advise what versions of Amber, Ambertools, MMPBSA
> > > > > > and what versions of Python
> > > > > > are compatible with Mac OS 10.11.6 (El Capitan) ?
> > > > > >
> > > > > >
> > > > > > Thanks so much!
> > > > > >
> > > > > >
> > > > > > Erik Zuiderweg
> > > > > > _______________________________________________
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Received on Wed Jan 04 2017 - 12:00:02 PST
