[Dock-fans] dock6 speed

Rima Chaudhuri rima.chaudhuri at gmail.com
Sat Oct 21 19:03:31 PDT 2006

I am trying to test a small sample of 300 molecules using dock6. The speed
is unbelievably slow, it takes almost 15 mins to read the frid files and
another 45 mins to dock 1 compound. I aim to dock huge databases later. I
think I might be doing something wrong w.r.t the input file, but that i
downloaded from the tutorial and made neccessary changes. Am pasting my
dock.in for your perusal. Please suggest, as in what might be going wrong?
ligand_atom_file                                             ./test300.mol2
limit_max_ligands                                             no
read_mol_solvation                                            no
write_orientations                                              no
write_conformations                                          no
skip_molecule                                                  no
calculate_rmsd                                                 no
rank_ligands                                                    yes
max_ranked_ligands                                        300
scored_conformer_output_override                     no
orient_ligand                                                    yes
automated_matching                                        yes
max_orientations                                             100
critical_points                                                    no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                                  yes
min_anchor_size                                               40
num_anchor_orients_for_growth                         100
number_confs_for_next_growth                           100
use_internal_energy                                          yes
internal_energy_att_exp                                      6
internal_energy_rep_exp                                      12
internal_energy_dielectric                                   4.0
use_clash_overlap                                            no
bump_filter                                                       no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                    no
contact_score_secondary                                    no
grid_score_primary                                              yes
grid_score_secondary                                         yes
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
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                             100
simplex_grow_max_iterations                                100
simplex_final_min_add_internal                               no
simplex_secondary_minimize_pose                         no
simplex_random_seed                                          0
atom_model                                                   all

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