[Dock-fans] how to increase number of docked conformations?

William Joseph Allen william.joseph.allen at gmail.com
Fri Mar 22 07:33:56 PDT 2013


Hi Chinh,

You did not do anything wrong - the "conformers.mol2" will give you all of
the successfully-grown conformers up to the number you specify with
"num_scored_conformers". The fact that only 22 were written to file likely
means that DOCK could only generate 22 complete molecule conformers that
were not pruned away (e.g. because of clashes or bad score).

Joe Allen



On Fri, Mar 22, 2013 at 5:50 AM, Chinh Su Tran To
<chinh.sutranto at gmail.com>wrote:

> Dear DOCK-fans,
>
> I need to increase the number of docked ligand conformations to 100 (from
> the 1st trial of 10), so I adjusted the "num_scored_conformers" to 100, but
> the results "conformers.mol2" only showed 22.
> How could that be? or Did I do something wrong?
>
> Below is my dock.in. Would anyone please help take a look?
>
> *ligand_atom_file
> ../data/lig.mol2*
> *limit_max_ligands                                            no*
> *skip_molecule                                                no*
> *read_mol_solvation                                           no*
> *calculate_rmsd                                               no*
> *use_database_filter                                          no*
> *orient_ligand                                                yes*
> *automated_matching                                           yes*
> *receptor_site_file                                           ./rec.sph*
> *max_orientations                                             500*
> *critical_points                                              no*
> *chemical_matching                                            no*
> *use_ligand_spheres                                           no*
> *use_internal_energy                                          yes*
> *internal_energy_rep_exp                                      12*
> *flexible_ligand                                              yes*
> *user_specified_anchor                                        no*
> *limit_max_anchors                                            no*
> *min_anchor_size                                              40*
> *pruning_use_clustering                                       yes*
> *pruning_max_orients                                          100*
> *pruning_clustering_cutoff                                    100*
> *pruning_conformer_score_cutoff                               25.0*
> *use_clash_overlap                                            no*
> *write_growth_tree                                            no*
> *bump_filter                                                  no*
> *score_molecules                                              yes*
> *contact_score_primary                                        yes*
> *contact_score_secondary                                      no*
> *contact_score_cutoff_distance                                4.5*
> *contact_score_clash_overlap                                  0.75*
> *contact_score_clash_penalty                                  50*
> *contact_score_grid_prefix                                    grid*
> *grid_score_secondary                                         no*
> *multigrid_score_secondary                                    no*
> *dock3.5_score_secondary                                      no*
> *continuous_score_secondary                                   no*
> *descriptor_score_secondary                                   no*
> *gbsa_zou_score_secondary                                     no*
> *gbsa_hawkins_score_secondary                                 no*
> *SASA_descriptor_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_grow_tors_premin_iterations                          0*
> *simplex_random_seed                                          0*
> *simplex_restraint_min                                        no*
> *atom_model                                                   all*
> *vdw_defn_file
>  /usr/local/apps/dock6/parameters/vdw_AMBER_parm99.defn*
> *flex_defn_file
> /usr/local/apps/dock6/parameters/flex.defn*
> *flex_drive_file
>  /usr/local/apps/dock6/parameters/flex_drive.tbl*
> *ligand_outfile_prefix                                        lig_dock*
> *write_orientations                                           yes*
> *num_scored_conformers                                        100*
> *write_conformations                                          yes*
> *cluster_conformations                                        yes*
> *cluster_rmsd_threshold                                       2.0*
> *rank_ligands                                                 yes*
> *max_ranked_ligands                                           500*
>
> Thank you very much.
>
> Regards,
> Chinh
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://mailman.docking.org/mailman/listinfo/dock-fans
>
>


-- 
William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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