Difference between revisions of "Virtual Screening Protocol on BlueGene (IGF-IR system)"

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set box_margin = 8</nowiki>
set box_margin = 8</nowiki>
(2)Dock to the subset of the database
(2) Dock to the subset of the database

Revision as of 21:05, 20 July 2012


1. Identify the target


2. Prepare the target


3. Database Preparation

4. Run Docking on Bluegene

(1) Make the grid for the protein. cat <<EOF >box.in yes $box_margin ./selected_spheres.sph 1 box.pdb EOF

cat <<EOF >grid.in compute_grids yes grid_spacing $grid_spacing output_molecule yes contact_score no chemical_score no energy_score yes energy_cutoff_distance 999 atom_model a attractive_exponent ${attractive} repulsive_exponent ${repulsive} distance_dielectric yes dielectric_factor 4 bump_filter yes bump_overlap 0.75 receptor_file ./receptor.mol2 box_file ./box.pdb vdw_definition_file ./vdw.defn chemical_definition_file ./chem.defn score_grid_prefix ./${system}.rec receptor_out_file ./${system}.rec.grid.mol2 EOF Among them, the parameters are set as follows: set grid_spacing = 0.3 set attractive = 6 set repulsive = 9 set box_margin = 8

(2) Dock to the subset of the database