VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 18 2005 - 12:16:30 CST

Hi,
  I've posted Python library binaries here which should fix this problem:
http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/

I'm out of town until March 28, in case this doesn't fully address
getting IED running with VMD 1.8.3, I'll answer further questions
when I return.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 01, 2005 at 03:54:24PM +0100, Stef wrote:
> In latest VMD 1.8.3 there is the Interactive Essential Dynamics plugin
> located in /usr/local/lib/vmd/plugins/noarch/python/ied
>
> I'm trying to load it into vmd :
> gopython /usr/local/lib/vmd/plugins/noarch/python/ied/ied.py
>
> But i'm stuck with this error message :
>
> vmd > gopython /usr/local/lib/vmd/plugins/noarch/python/ied/ied.py
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "VMD", line 19, in ?
> ImportError: No module named vmdnumpy
>
> Whereas i have the module numpy on my computer :
> /usr/lib/python2.3/site-packages/Numeric/_numpy.so
>
> My system is Mandrakelinux 10.1 Official with :
>
> libpython2.3-2.3.4-6.1.101mdk
> python-numeric-23.1-2mdk
> python-2.3.4-6.1.101mdk
> libpython2.3-devel-2.3.4-6.1.101mdk
> python-base-2.3.4-6.1.101mdk
> python-gtk-0.6.11-6mdk
> python-gtk-devel-0.6.11-6mdk
>
> Could it be that a path is missing ?
> While commenting the firsts vmd-specific lines of the program :
> line 19 : #import molecule,vmdcallbacks,vmdnumpy,trans,animate,graphics
> line 20 : #import Molecule
>
> I can get the script running :
> [stephane_at_bioinfo ied-2.02]$ python2.3 ied_test.py
>
> Interactive Essential Dynamics v 2.0 (http://mccammon.ucsd.edu/ied)
> Copyright John Mongan <jmongan_at_mccamon.ucsd.edu>, 2003, 2004
>
> Citation: Interactive Essential Dynamics. John Mongan. Journal of
> Computer-Aided Molecular Design. In press.
>
> This library is provided under the LGPL with ABSOLUTELY NO WARRANTY.
>
> There is probably one initialisation part missing in gopython, but i've
> not found where as for now.
>
> Thanks a lot in advance for the help.
>
> Stéphane Teletchéa
> --
> http://www.steletch.org
> Fingerprint: 1E83 26EE A2F1 87E5 5865 4DBF F2B4 9083 F44C AE88
> GPG key @ http://www.steletch.org/article.php3?id_article=13
> Mandrakelinux release 10.1 (Official) @ http://www.mandrakesoft.com/
> 15:36:45 up 7:15, 1 user, load average: 2.27, 1.98, 1.53 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078