Subject: Re: CCL:AutoDock and protein-protein interactions

From: Richard Gillilan <reg8-.at.-cornell.edu>
Date: Wed, 9 Jul 2003 11:23:49 -0400

> * a more specific question:
> A way of circumventing a huge grid would be to use a smaller grid
> (assuming that the interacting residues must be 'close' to the 
> receptor)
> and setting the extnrg parameters to 0.0 kcal mol-1 (meaning that atoms
> outside the grid would feel no field). Is this a correct assumption?
> Would this speed up the calculations?
>

I've done a bit of work on hierarchical grids ... it can
be done for linear interpolation, but higher order interpolations
pose some problems. Once I started doing a lot of docking,
I found that, for most proteins, grid size is not a problem
if you work in the principle axis coordinate system (obtained
by diagonalizing the inertial matrix). A cubic grid constructed
using maximum extents + a buffer length along those axes will save a 
dramatic
amount of space. Van der Waals grids die to zero much beyond 5A from 
the surface.
Electrostatic protentials need to be larger. I go out
20A from the surface with my grid, then use the multipole approximation
beyond that point to infinity. Total sum of grids (one electrostatic and
5 VDW in double precision) usually amount to only a couple hundred MB 
at 0.6A grid spacing.
(for linear interpolation, one might want a finer grid). Single 
precision could work
just fine if storage is a problem. One would have to put up with the 
cost of type
conversion however. The grids do add up if you do a lot. I gridded the 
whole protein-protein docking
benchmark of 58 structures (check out the ZDOCK web pages). It was 
quite a few GB.

Richard Gillilan
MacCHESS, Cornell

ps, I just came back from the protein-protein docking meeting at 
Stonybrook a week
ago. If there is interest, I suppose I could post a brief report.