[Dock-fans] Protein-Protein Docking
sbrozell at scripps.edu
Thu Sep 18 18:11:58 PDT 2008
On Mon, 1 Sep 2008, CJ Arthur wrote:
> I've been trying to dock two proteins using Dock and have hit some
> problems. If possible could someone have a look at what I'm doing an tell
> me what I'm doing wrong please.
Grepping for ligand_center and match_receptor in the source code
finds only lines in program grid.
Grepping for use_ligand_spheres and ligand_sphere_file in the source code
finds only lines in program dock.
Thus, Macromolecular Docking as described in the manual appears
to need both corrections (ligand_centers -> use_ligand_spheres,
ligand_center_file -> ligand_sphere_file, and match_receptor_sites seems
to have been redundant and merely replaced with automated_matching=no)
and completion (there may be steps involving grid that are not described).
I'm adding an investigation of this to the todo list.
But maybe the grid clues are enough for you to figure this out.
Unfortunately, it looks like the only documentation for this aspect of grid
is its source code.
Also I may be all wrong regarding grid. I've never tried macromolecular
DOCKing. As a final thought, start small and scale up.
Please follow up since I want to at least correct the documentation
such as it is.
> Can anyone see what I'm doing wrong, or can someone send me the grid and
> dock input files that they have used previously so that i can try to get
> an idea of where i'm making my mistake.
> Thanks in advance.
> I generate spheres around both my recetor and ligand proteins using sphgen
> i then select spheres around the active site of the receptor, so that the
> ligand is placed in an appropriate place
> sphere_selector receptor.sph activesite.mol2 10.0
> and make a pdb file of selected_spheres.sph so that i can check it in chimera
> i then use showbox with a margin of 50A, so that its big enought to hold
> my ligand molecule.
> I then use grid with the grid input settings listed below
> And then I dock using the dock settings listed below.
> What happens is that the ligand molecule is overlayed over the receptor
> (its as iff the the ligand is put 'into' the spheres of the receptor.
> grid input
> 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 receptor.mol2
> box_file site_box.pdb
> vdw_definition_file /home/chxcja/dock6/parameters/vdw_AMBER_parm99.defn
> score_grid_prefix grid
> dock input
> ligand_atom_file ligand.mol2
> limit_max_ligands no
> skip_molecule no
> read_mol_solvation no
> calculate_rmsd no
> orient_ligand yes
> automated_matching no
> distance_tolerence 0.25
> distance_minimum 2.0
> nodes_minimum 3
> nodes_maximum 10
> receptor_site_file activesite.sph
> max_orientations 500
> critical_points no
> chemical_matching no
> use_ligand_spheres yes
> ligand_sphere_file ligand.sph
> flexible_ligand no
> bump_filter yes
> bump_grid_prefix grid
> max_bumps_anchor 1
> max_bumps_growth 1
> score_molecules yes
> contact_score_primary no
> contact_score_secondary no
> grid_score_primary no
> grid_score_secondary yes
> grid_score_rep_rad_scale 1
> grid_score_vdw_scale 1
> grid_score_es_scale 1
> grid_score_grid_prefix grid
> dock3.5_score_primary no
> continuous_score_primary yes
> cont_score_rec_filename receptor.mol2
> cont_score_att_exp 6
> cont_score_rep_exp 12
> cont_score_rep_rad_scale 1
> cont_score_use_dist_dep_dielectric yes
> cont_score_dielectric 4.0
> cont_score_vdw_scale 1
> cont_score_es_scale 1
> minimize_ligand no
> atom_model all
> ligand_outfile_prefix complex_out
> write_orientations yes
> num_primary_scored_conformers_rescored 10
> write_primary_conformations yes
> cluster_primary_conformations yes
> cluster_rmsd_threshold 2.0
> num_clusterheads_for_rescore 5
> num_secondary_scored_conformers 5
> write_secondary_conformations yes
> rank_primary_ligands no
> rank_secondary_ligands no
More information about the Dock-fans