[Dock-fans] Dock is too slow even in parallel using MPI

Phan, Jason jason.phan at Vanderbilt.Edu
Tue Apr 17 10:13:59 PDT 2012

Hi Trent,

Thanks for the suggestion and sample input file. We're in the process of upgrading to dock6.mpi. I cut down everything to a bare minimum e.g. max_orientations 25, min_anchor_size 40, num_anchor_orients_for_growth 50, num_confs_for_next_growth 50, simplex_anchor/growth_max_iterations 100. I have a very well-defined pocket for a big ring so I don't need too many initial orientations. So far the energy score comes down a little bit and more rejections due to lack of orientations but the speed is up a lot, ~10x. I'll view the poses when it's done to see if it makes sense.


On Apr 17, 2012, at 8:35 AM, Trent E. Balius wrote:

Hi Jason,

My first suggestion is to upgrade to DOCK v6.5 the latest release which has the latest features and code improvements.

1-3 min per ligand seams about right for on-the-fly growth in DOCK5 and DOCK6.
Both DOCK 5 and 6 are slower than DOCK 4, but have a higher success rate in pose reproduction experiments.

Note that the MPI implementation of dock is designed for virtual screening applications.  DOCK will distribute molecules to different nodes. DOCK does not parallelize the growth of individual molecules.
See the following:

The other parameters that impact the speed (but also sampling) are:

flexible_ligand                                              yes
min_anchor_size                                              5
pruning_use_clustering                                       yes
pruning_max_orients                                          1000
pruning_clustering_cutoff                                    100
pruning_conformer_score_cutoff                               100.0

min_anchor_size  40 only one anchor is used.  min_anchor_size 5 all rings are used.

pruning_max_orients is the maximum number of anchor orientations carried forward in the anchor & grow search (previously num_anchor_orients_for_growth)

pruning_clustering_cutoff  is the number of orients retained at each stage of growth referred to as N_c in the equation in Pruning the Conformation Search Tree.

See  Manual:


The following is an example virtual screening script used by the Rizzo Group to good effect on a BlueGene.

ligand_atom_file                                             cdiv.sub01.100000.CH001.mol2
limit_max_ligands                                            yes
max_ligands                                                  60000
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          yes
max_heavy_atoms                                              1000
min_heavy_atoms                                              0
max_rot_bonds                                                15
min_rot_bonds                                                0
max_molwt                                                    10000
min_molwt                                                    0
max_formal_charge                                            2
min_formal_charge                                            -2
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           rec.clust.close.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
flexible_ligand                                              yes
min_anchor_size                                              5
pruning_use_clustering                                       yes
pruning_max_orients                                          1000
pruning_clustering_cutoff                                    100
pruning_conformer_score_cutoff                               100
use_clash_overlap                                            no
print_growth_tree                                            no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_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
restraint_min                                                no
atom_model                                                   all
vdw_defn_file                                                vdw_AMBER_parm99.defn
flex_defn_file                                               flex.defn
flex_drive_file                                              flex_drive.tbl
ligand_outfile_prefix                                        cdiv.sub01.CH001.dock2grid
write_orientations                                           no
num_scored_conformers                                        1
write_conformations                                          no
rank_ligands                                                 no

I hope that this helps,

Trent E. Balius
Graduate Student, Rizzo Group
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

-----Original Message-----
From: Phan, Jason <jason.phan at Vanderbilt.Edu<mailto:jason.phan at Vanderbilt.Edu>>
To: dock-fans <dock-fans at docking.org<mailto:dock-fans at docking.org>>
Sent: Mon, Apr 16, 2012 8:41 pm
Subject: [Dock-fans] Dock is too slow even in parallel using MPI

Dear All,

What are the parameters that can be manipulated to improve the virtual docking
performance without compromising the quality of the dock results? My grid box is
pretty small, covering ~11 spheres and pretty much default values were used for
all the parameters. Using parallel processing with dock5mpi over 4 nodes, 8
processors each, the speed is terribly slow, e.g. 1-3 min per ligand. I tried
lowering the  max_orientations, simplex iterations, 1 conformer written, no
clustering etc... and it improved some. I'm wondering if there are better ways
to speed things up a lot more.

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20120417/aaa68913/attachment-0001.html 

More information about the Dock-fans mailing list