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

Chinh Su Tran To chinh.sutranto at gmail.com
Fri Mar 22 19:20:44 PDT 2013


Dear Allen,
Thank you for your explanation.

Chinh

On Friday, March 22, 2013, William Joseph Allen wrote:

> 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 <javascript:_e({}, 'cvml',
> '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_rest*
>> _______________________________________________
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>> Dock-fans at docking.org <javascript:_e({}, 'cvml',
>> '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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