[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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>   
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