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 - 11:30:03 PST
