Re: [AMBER] About python usage in AmberTools

From: Hai Nguyen <>
Date: Tue, 7 Jul 2015 14:33:42 -0400


I can answer question about `pytraj`.

This error "undefined symbol: _ZN14MaskTokenArray13SelectedChar_E" likely
indicates that you have old `` file somewhere.

Since `pytraj` is in dev-status, it catch up with `cpptraj-dev` version and
not work with version in official AT15.

Can you try running this script from here:

and let us know the output.

Alternative, you can install from github (the most updated version).

*git clone
<>cd pytrajpython ./ install*

(`pytraj` will install `cpptraj-dev` from github for you. Make sure to read
the instruction after the install finish)


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?
> 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).
> I've a second question also related to python. I've tried to install the
> pytraj program on my conda distribution like the Amber Manual suggests:
> conda install --force -c pytraj pytraj-dev
> And it installs it correctly in my anaconda3 folder. Now if I open the
> python interpreter and import pytraj, I get the following error
> . I don't know if this might be
> related to the problems I've reported before? Or it could be an issue
> related to the Cython code that's in pytraj? Just a guess based on my
> little experience with python.
> I'm pretty stuck on this so any guidance on this matter would be
> appreciated,
> Juan Eiros
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Received on Tue Jul 07 2015 - 12:00:02 PDT
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