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

Trent E. Balius tbalius at aol.com
Fri Mar 22 07:47:27 PDT 2013

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:

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.

I hope this helps,



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
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.

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