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

Chinh Su Tran To chinh.sutranto at gmail.com
Fri Mar 22 02:50:27 PDT 2013


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
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