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

Chinh Su Tran To chinh.sutranto at gmail.com
Fri Mar 22 19:18:49 PDT 2013


Dear Dr. Balius,
Thank you very much. Those are really what I need.

Chinh

On Friday, March 22, 2013, Trent E. Balius wrote:

>   *Hi Chinh,
>
> These are the parameters you need to change to effect sampling**
> *
> *  max_orientations                                           500
>
>   min_anchor_size                                           40**
>   pruning_use_clustering                                  yes**
>   pruning_max_orients                                     100**
>   pruning_clustering_cutoff                               100**
>   pruning_conformer_score_cutoff                     25.0
> *
> *
> I would recommend changing them to the following:
> *
> *  max_orientations                                             500
>
> *  *min_anchor_size                                              5**
>   pruning_use_clustering                                     yes**
>   pruning_max_orients                                        100**
>   pruning_clustering_cutoff                                  500**
>   pruning_conformer_score_cutoff                        200.0
> *
>
> The following parameter controls the final clustering and does not effect
> sampling but will effect the output conformations in the scored file:
> *  cluster_rmsd_threshold                                  2.0*
> change clustering cut-off to
> *  cluster_rmsd_threshold                                  0.5
> *
>
>
>
> See the following for further discussion of this parameters:
>   http://mailman.docking.org/pipermail/dock-fans/2012-April/002650.html
>   http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand
>   http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility
>   http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
>
> Change them yourself and see how they effect sampling.
> You may want to use the verbose flag to help understand how modifying the
> above parameters effect growth.
>
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GrowthTreeAndStatistics
>
> I hope this helps,
>
> Trent
>
>  ======================================
> Trent E. Balius, PhD
> Shoichet Lab – Dept. of Pharm Chem,
> University of California, San Francisco
> 1700 4th Street
> Box 2550
> San Francisco, CA 94158
> Office: Byers Hall, Rm 509
> URL: http://docking.org/~tbalius
> ======================================
>
>
>  -----Original Message-----
> From: Chinh Su Tran To <chinh.sutranto at gmail.com>
> To: dock-fans <dock-fans at docking.org>; me <chinh.sutranto at gmail.com>
> Sent: Fri, Mar 22, 2013 2:50 am
> Subject: [Dock-fans] how to increase number of docked conformations?
>
>  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*
>
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