From: Cook, Rich (
Date: Mon Aug 26 2013 - 18:44:26 CDT

I have downloaded and installed the binary release of VMD 1.9.1 on our clusters and one of our users pointed out that "python in VMD is broken" on our machines.
There are two symptoms:
1) import os,sys fails, as shown by the output below of vmd -python
rcook_at_rzgpu2 (vmd-1.9.1): vmd -python
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
blah blah blah…
Info) Starting Python...
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ValueError: vmdnumpy module not available.
Info) Text interpreter now Python
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/tools/vmd-1.9.1/lib/vmd/scripts/python/", line 59, in <module>
    import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter
>>> import os,sys
Traceback (most recent call last):
  File "VMD", line 1, in <module>
ImportError: No module named os
I've tried fiddling with PYTHONHOME and such and either I'm doing that wrong or that's not the right approach. Can anyone solve this?

2) readline does not work in vmd. I.e., up arrow does not get the last command, etc. Can this be fixed without a recompile?

✐Richard Cook
✇ Lawrence Livermore National Laboratory
Bldg-453 Rm-4024, Mail Stop L-557
7000 East Avenue, Livermore, CA, 94550, USA
☎ (office) (925) 423-9605
☎ (fax) (925) 423-6961
Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
(opinions expressed herein are mine and not those of LLNL)