[Dock-fans] Write multiple conformations during parallel processing

Sudipto Mukherjee sudmukh at yahoo.com
Fri Jul 16 10:04:07 PDT 2010

Dear Cen,

A maximum of 3 docked conformers will be written to prefix_scored.mol2
Nothing will be written to prefix_confomer.mol2 with write_conformations set to 

In your case, what is happening is that after scoring, pruning and clustering, 
only one viable docked conformation remains. You will get up to 3 conformations 
in prefix_scored.mol2 if you keep trying with different ligands. I suggest that 
try this with a small database of 1000 ligands instead of just docking in one 
molecule. You should that many of them will have 2 or more conformers in the 
prefix_scored.mol2 file. 

For your reference, here is the dock input file I used to verify this:

orient_ligand                                                yes
automated_matching                                           yes
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                               100.0
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                                       121P.rec
dock3.5_score_secondary                                      no
continuous_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
atom_model                                                   all
flex_defn_file                                               flex.defn
flex_drive_file                                              flex_drive.tbl
ligand_outfile_prefix                                        flex.dock2grid
write_orientations                                           no
num_scored_conformers                                        1
write_conformations                                          no
rank_ligands                                                 no

Sudipto Mukherjee
Trent E. Balius
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University

From: Cen Gao <cengao at gmail.com>
To: Sudipto Mukherjee <sudmukh at yahoo.com>
Cc: Dock-fans at mailman.docking.org
Sent: Thu, July 15, 2010 6:03:42 PM
Subject: Re: [Dock-fans] Write multiple conformations during parallel  

Hi Sudipto:

Thanks for the email. I have tried to set  "num_scored_conformer" to 3 and 
"write_conformations" to No before, but it still generated only one pose per 
molecule to prefix_scored.mol2, while never wrote anything to 
prefix_confomer.mol2. May I ask whether this setting works differently on your 
version of DOCK?  (I am using DOCK6.4, compiled with GCC4.1)  Or are there any 
parameters I should set?

If I set write_conformations to yes, it was able to write 1 pose to 
prefix_scored.mol2 and 3 poses per molecule into prefix_confomer.mol2 as 
expected. But again it works in serial version of DOCK only, but refuses to run 
in parallel.



On Thu, Jul 15, 2010 at 5:21 PM, Sudipto Mukherjee <sudmukh at yahoo.com> wrote:

Hi Cen,
>As you mentioned in your email, the "num_scored_conformer" is the parameter you 
>want to use. 
>Set this to 3 as you wish. 
>Set "write_conformations" as no. By default this is yes. The naming convention 
>is a bit confusing here, I admit. The write_conformations parameter writes out 
>partial conformers in a separate conformers.mol2 Setting this parameter to yes 
>is what geenrates the ERROR about filling up the disk during mpi runs. 
>Now you should have a maximum of 3 conformers for each molecule screened. 
> Regards
>Sudipto Mukherjee
>Graduate Student,  Robert C. Rizzo Lab
>Dept. of Applied Math & Statistics, Stony Brook University
From: Cen Gao <cengao at gmail.com>
>To: Dock-fans at mailman.docking.org
>Sent: Tue, July 13, 2010 12:13:53 PM
>Subject: [Dock-fans] Write multiple conformations during parallel processing
>Dear Dock fans:
>May I ask is it possible for DOCK to write out the top N conformers for each 
>molecule it processed during the parallel docking run? The manual states that 
>this feature is only available to serial version of DOCK to "protect against 
>filling up the disk", as "in conformer.mol2, the number of molecules in the 
>output file will be equal to the database size * the number of anchors per 
>molecule * the number of conformations that pass the final pruning stage * the 
>number of conformers per cycle."  
>But if I understand it right, this conformer number should not be that huge as 
>it is something we can control using the keyword "num_scored_conformer" (in the 
>case of primary_score only), right?  As long as I set this keyword to a smaller 
>value, say 3 or 5, it will only write 3 or 5 poses per molecule, which will not 
>be a problem in case of the file size. Did I miss something here?

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