VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 23 2005 - 10:22:28 CDT

Hi,
  You could calculate the overlapping volume in several ways, one would be
to use the VDW radii and atom coordinates to find sphere intersectinos and
such, another would be to calculate surfaces and do intersections between
the surfaces, a very easy but cheesy method would be to calculate a voxel
grid marking individual voxels by adding 1 when they are contained within a
VDW sphere or surface. You could then go back and easily estimate the volume
of the overlap by summing up the number of voxels that have a count of 2 or
more. There'll definitely be error since it's a discrete sampling of space,
but it's easy to implement, so it might be a useful crude measure to see
if this information is very useful before you go doing something much more
laborious and time consuming that yields exact answers.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 21, 2005 at 12:01:04AM -0700, Brian Kidd wrote:
> Hello All,
>
> I'm looking for a way to calculate the overlapping area between two
> molecules. Is there a way use the van der wall radii or something else
> to calculate this area? I'd specifically like to select residues on two
> different molecules and determine whether they've collided or not when
> I align them and then quantify this collision - say the area of
> overlap.
>
> Thanks,
> -Brian 

-- 
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