Re: [AMBER] About python usage in AmberTools

From: Eiros Zamora, Juan <>
Date: Tue, 7 Jul 2015 19:50:45 +0000

Hi Jason,

So once I've created the environment py27 with conda, how do I use it with Amber?

I don't have access to my workstation right now, but should it be something like

./configure --with-python py27
make install

I prefer to do that rather than forcing it to use Python 3, as I would like to make full use of the AmberTools programs.

Thanks for the info,

De: Jason Swails []
Enviado: martes, 07 de julio de 2015 19:55
Para: AMBER Mailing List
Asunto: Re: [AMBER] About python usage in AmberTools

On Tue, Jul 7, 2015 at 2:05 PM, Juan Eiros Zamora <> wrote:

> Hi Amber users,
> I've recently downloaded AmberTools15 and followed all the installation
> steps succesfully on a RHEL6. But when I try to do
> make test
> I get the following errors (copied
> in this link)
> The python version that I currently use is 3.4.3 installed with Anaconda
> 2.1.0 (64-bit) distribution. Also my PYTHONPATH is set to
> /usr/local/amber15/lib/python2.7/site-packages:/usr/local/amber/lib/python2.7/site-packages
> after I source the $AMBERHOME/ script.
> So what's the python that AmberTools is trying to use? And how do I
> manage to add python packages to the AmberTools installation?

Most of Amber's Python tools are written for Python 2. Some of them are
Python-3 compatible (I know ParmEd can be installed with Python 3, and I
*think* will work as well), but others are probably not.

So the configure script looks for python2.7, python2.6, python2.5,
python2.4, and falls back to python if none of the previous choices are
available. You can always use conda to set up a new Python 2.7 virtual

conda create -n py27 python=2.7

And use that environment with Amber.

If you want to force AmberTools to use your anaconda Python 3, you can use
"--with-python `which python`" when you run configure.

> I've previously experienced problems with other AmberTools
> programs, such as, or, (see errors here
> ) in which python modules are
> missing; and I don't know how to add them because if I just do conda
> install package it will install it in my regular python distribution
> (although that the _tkinter that's missing I can't even find it using
> conda).

​conda should come with Tkinter already installed.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 07 2015 - 13:00:03 PDT
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