VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 15 2004 - 16:45:38 CDT

Jerry,
  Thanks for the test dataset.
I don't know when I'll be able to work on this, but we _should_ be able
to come up with a means for extending our plugin system to allow for
multi-molecule structure files, though there's no provision for this
at the moment. Once I finish a few other things I'll take a look
at the features you suggest. It'll probably be easy to add hooks
in the plugin system for reporting availability of multiple structures,
but tricky to work out the user interface (and particularly text interface)
issues that result from such a change.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 14, 2004 at 07:54:09PM +0000, Jerry Ebalunode wrote:
> Hi John,
> Attached is the sample mol2 file, you requested. It contains structural
> information for 10 different compounds. Most compound database docking
> programs e.g. DOCK and FRED, report the docked ligand pose to a receptor
> structure in this format. So ideally each ligand should be read in
> differently as a new molecule in VMD. This will allow us to look at each
> docked ligand in context of the receptor (assuming that the receptor
> structure was loaded into VMD previously). Could it be possible implement
> inter molecule (different mol ID) h-bond calculations within future
> versions of VMD, I know for now that VMD is limited to doing intra h-bond
> molecule calculations. This will go hand in hand in visualizing and analyzing
> all the docked compounds in the mol2 file. Thanks. 

-- 
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