[Dock-fans] dock6 speed

Sudipto Mukherjee sudmukh at yahoo.com
Tue Oct 24 08:15:20 PDT 2006

Dear Rima,

I noticed you set max_orientations to be only 100, and all the other parameters seem quite reasonable. I do not think dock is running so slow because of the input file. However, dock may take a long time if your SPH file has a large number of spheres. Make sure the docking spheres are actually in the binding site, and the final_spheres.sph has a reasonable number of spheres (consider using sphere_selector with a 10A cutoff). 

Apart from that, it is possible that Unix machine you are using might be old and slow. Since it takes 15 mins to read in the grid files, I think reading from the disk might be slow. Could you send the details of the computer you are using to run dock? 

Sudipto Mukherjee

----- Original Message ----
From: Rima Chaudhuri <rima.chaudhuri at gmail.com>
To: dock-fans at docking.org
Sent: Saturday, October 21, 2006 10:03:31 PM
Subject: [Dock-fans] dock6 speed


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
ligand_outfile_prefix                                        flex_lig_may_test
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
receptor_site_file                                           ./final_spheres.sph 

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
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_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

vdw_defn_file                                                /hprog/dock6/parameters/vdw_AMBER_parm99.defn 
flex_defn_file                                               /hprog/dock6/parameters/flex.defn
flex_drive_file                                              /hprog/dock6/parameters/flex_drive.tbl



Dock-fans mailing list
Dock-fans at docking.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20061024/0b216968/attachment.html

More information about the Dock-fans mailing list