From: Sacerdoti, Federico (
Date: Tue Apr 04 2006 - 11:11:16 CDT


I have installed vmd 1.8.3 on our Linux x86_64 (Rocks 4.0 - Centos
4.2/RHEL4 based) systems. I notice that vmd has its own compiled in
version of python, which is an older version than the RHEL4 standard:

vmd 1.8.3:

>>> import sys
>>> sys.version
'2.2.2 (#1, Jan 31 2005, 10:19:19) \n[GCC 3.3.3 20040412 (Red Hat Linux


>>> import sys
>>> sys.version
'2.3.4 (#1, Feb 17 2005, 21:01:10) \n[GCC 3.4.3 20041212 (Red Hat

This of course causes lots of problems. Right off the bat _tkinter
cannot be found, although the native python has no problems with it.

I have installed your precompiled python libraries from

But that does not help with _tkinter, since it does not seem to be
included. Perhaps that is due to this unanswered thread:

As for Numeric, if I set the PYTHONPATH to something appropriately
then vmd can find Numeric, but there is still an error:

vmd > gopython
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>]
/usr/lib64/python2.3/ Warning: 'yield' will become a reserved
keyword in the future
'import site' failed; use -v for traceback

Numeric Python module _numpy not found; vmdnumpy module not available.
hon2.2/site-packages/Numeric/ undefined symbol: _Py_NoneStruct

Info) Text interpreter now Python
Traceback (most recent call last):
  File "<string>", line 1, in ?
line 59, in ?
    import _tkinter # If this fails your Python may not be configured
for Tk
ImportError: No module named _tkinter

Was the library compiled incorrectly, or did I do something wrong during


D.E. Shaw Research LLC
New York