[Dock-fans] Generating grid for big molecules

[John J. Irwin]

Hi Francesco

We usually make grids over a 30x30x30 Angstrom box at 3 grid points per
Angstrom, centered on and covering the binding site. I make that about
729K grid points. Even if you doubled it, which would be *huge* and
generally *unnecessary*, you get 5.8 M grid points. I just don't
understand why you are making such a big box and big grids.

John
UCSF DOCK Team

Francesco Pietra wrote:
> 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
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