[Dock-fans] Generating grid for big molecules

[Francesco Pietra]

I wonder whether the advancement in programming would now allow to
improve on the speed of program "grid", particularly as little use of
RAM memory is currently made by the program.

With about 10 million grid points I had no problems; completed in a
couple of hours. With 60 million points (a grid box of 153 110 108 A)
it may be impracticably too slow. It is only after 600 minutes
(measured with "top -i") that some percent of protein atoms have
progressed (a miserable 10%), while comparatively little memory is
used (3.6% of 24GB) . Clearly th engagement is not linear.

As I want to examine the whole protein, I am thinking to create
smaller grids for the various parts of the protein, rather than
re-modeling by cutting parts of the protein away. Right?

Here is the grid script I am using. Could it be adapted to the heavy
task of this protein while not triggering false docking?

===============
grid.in

compute_grids                  yes
grid_spacing                   0.3
output_molecule                no
contact_score                  no
energy_score                   yes
energy_cutoff_distance         9999
atom_model                     a
attractive_exponent            6
repulsive_exponent             12
distance_dielectric            yes
dielectric_factor              4
bump_filter                    yes
bump_overlap                   0.75
receptor_file /home/francesco/dockwork/dock_charge-53/mod21_r_c.mol2
box_file  /home/francesco/dockwork/dock_charge-53/mod21_272A_75.pdb
vdw_definition_file /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
score_grid_prefix              grid
=========================


Thanks
francesco pietra