[Dock-fans] Problems with Max_orientations and intramolecular clashes with Dock 6.2/DUD
John J. Irwin
jji at cgl.ucsf.edu
Thu May 14 10:55:01 PDT 2009
Hi Vidana
There is a new release of DOCK on its way that fixes this problem. I
don't want to rush the people putting this release together, but they
know who they are, and I am hereby encouraging them to enlist you to
help them test it (and you get this problem fixed at the same time).
John
Vidana.Epa at csiro.au wrote:
>
> Hi all,
>
>
>
> Further to the Max_orientations problem that I reported
> yesterday (target: Neuraminidase, ligands from DUD database, flexible
> ligand docking with Dock 6.2), I took a molecule (ZINC03889009) that
> had been earlier docked with max_orientations set at 5000, and
> increased this value to 50000. To my surprise, it failed to dock,
> giving the error message “Could not complete growth. Confirm that the
> grid box is large enough to contain the ligand, and try increasing
> max_orientations”. (!) I am puzzled as to how this could be.
>
>
>
> Then, when I inspected the earlier (i.e.
> max_iterations=5000) docking with this molecule, I find that there are
> serious steric clashes inside the molecule in the docked pose (absent
> in the input conformation), with a couple of non-bonded atoms just
> 0.35 A apart. So, the ‘successful’ docking is an error as well.
> Shouldn’t the internal energy van der Waals term have prevented this
> from happening in the growth phase? As you can see from below, the
> input is pretty basic.
>
>
>
> Any suggestions/comments?
>
>
>
> Thanks very much.
>
>
>
> Cheers,
>
>
>
> Vidana.
>
>
>
>
>
> ligand_atom_file
> dudp1lig_t3_1446.mol2
>
> limit_max_ligands no
>
> skip_molecule no
>
> read_mol_solvation no
>
> calculate_rmsd yes
>
> use_rmsd_reference_mol yes
>
> rmsd_reference_filename
> dudp1lig_t3_1446.mol2
>
> orient_ligand yes
>
> automated_matching yes
>
> receptor_site_file
> sphgen_cluster1_final.sph
>
> max_orientations 5000
>
> critical_points no
>
> chemical_matching no
>
> use_ligand_spheres no
>
> flexible_ligand yes
>
> min_anchor_size 40
>
> pruning_use_clustering yes
>
> pruning_max_orients 100
>
> pruning_clustering_cutoff 100
>
> use_internal_energy yes
>
> internal_energy_att_exp 6
>
> internal_energy_rep_exp 12
>
> internal_energy_dielectric 4.0
>
> use_clash_overlap no
>
> bump_filter yes
>
> bump_grid_prefix grid_r10
>
> max_bumps_anchor 2
>
> max_bumps_growth 2
>
> score_molecules yes
>
> contact_score_primary no
>
> contact_score_secondary no
>
> grid_score_primary yes
>
> grid_score_secondary no
>
> grid_score_rep_rad_scale 1
>
> grid_score_vdw_scale 1
>
> grid_score_es_scale 1
>
> grid_score_grid_prefix grid_r10
>
> dock3.5_score_secondary no
>
> continuous_score_secondary no
>
> gbsa_zou_score_secondary no
>
> gbsa_hawkins_score_secondary no
>
> amber_score_secondary no
>
> minimize_ligand yes
>
> minimize_anchor yes
>
> minimize_flexible_growth yes
>
> use_advanced_simplex_parameters no
>
> simplex_max_cycles 1
>
> simplex_score_converge 0.1
>
> simplex_cycle_converge 1.0
>
> simplex_trans_step 1.0
>
> simplex_rot_step 0.1
>
> simplex_tors_step 10.0
>
> simplex_anchor_max_iterations 500
>
> simplex_grow_max_iterations 500
>
> simplex_final_min no
>
> simplex_random_seed 0
>
> atom_model all
>
> vdw_defn_file
> /software/dock6.2/parameters/vdw_AMBER_parm99.defn
>
> flex_defn_file
> /software/dock6.2/parameters/flex.defn
>
> flex_drive_file
> /software/dock6.2/parameters/flex_drive.tbl
>
> ligand_outfile_prefix
> dudp1lig_t6_1446c
>
> write_orientations no
>
> num_scored_conformers 1
>
> rank_ligands no
>
>
>
>
>
>
>
>
>
>
>
> Vidana C. Epa
>
>
>
> CSIRO,
>
> Division of Molecular Health & Technologies,
>
> 343 Royal Parade,
>
> Parkville, Victoria 3052,
>
> AUSTRALIA.
>
>
>
> tel: (61) - 3 - 9662 - 7345
>
> fax:(61) - 3 - 9662 - 7347
>
>
>
> email: Vidana.Epa at csiro.au
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
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> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
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