[AMBER] About python usage in AmberTools

From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
Date: Tue, 07 Jul 2015 19:05:23 +0100

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 http://lpaste.net/42814355720372224 (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
after I source the $AMBERHOME/amber.sh 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 xparmed.py, or mdout_analyzer.py, (see errors here
http://lpaste.net/7336825506265825280 ) 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

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
http://lpaste.net/3868115149562839040 . 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

Juan Eiros

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Received on Tue Jul 07 2015 - 11:30:02 PDT
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