[Dock-fans] Scoring and parallel processing problems

Terry Lang terry at cgl.ucsf.edu
Thu May 11 13:30:25 PDT 2006


Dear Dmitry,

       Continuous scoring take at least an order of magnitude longer 
than grid-based scoring, which is why most people use grid score for 
docking.  When you say "hang," how long did you let it go for?  Is it 
possible it was still running?
       GBSA also takes a long time to run, and we would also only 
recommend GBSA for rescoring after docking is complete rather than for 
use during docking.  The warnings that are being printed in your outfile 
right now unfortunately cannot be suppressed in the current release of 
DOCK.  However, if you only use GBSA for rescoring, the number of 
warnings will be greatly reduced.
       In most cases, differences in energy values between operating 
systems is the result of insufficient sampling.  The parameters that are 
currently recommended are only optimized for molecules with up to seven 
rotatable bonds.  For these molecules, we have tried docking on a 
variety of systems and found the values to be the same within about one 
decimal place.  However, if your molecules have more than 7 rotatable 
bonds, you will probably need to sample more to get that type of robustness.

Sincerely,
Terry

Dmitry Osolodkin wrote:

>Hello all.
>I have three problems with Dock 5.4. Contact and energy scoring works fine, 
>but...
>1. ...When I try to use continuous scoring, Dock hangs when reading the bump 
>grid. Outfile is cont.out (attached).
>2. ...When I try to use gbsa scoring, it simply does not work and produces 
>extremely large outfile (the head of this file is attached as gbsa.out). The 
>grids were created exactly as described in the tutorial for the version 5.2. 
>Is there any newer tutorial?
>3. ...When I try to perform virtual screening, there are rather different 
>results on an Intel PC single machine (precompiled version) and on AMD 
>Opteron cluster (compiled with PGI compiler). Energy value differs up to 2 
>kcal/mol between two machines, and it changes the ranking significantly. The 
>same problem appears when I use contact scoring. Continuous and gbsa scoring, 
>as you can understand, don't work. Is there any solution of the problem?
>
>Best wishes,
>Dmitry Osolodkin
>  
>
>------------------------------------------------------------------------
>
>
>
>
>--------------------------------------
>DOCK v5.4.0
>
>Released March 2006
>Copyright UCSF
>Authored by:
>	Tack Kuntz
>	Demetri Moustakas
>	Paula Therese Lang
>	Scott Pegg
>	Scott Brozell
>--------------------------------------
>
>
>Molecule Library Parameters
>------------------------------------------------------------------------------------------
>ligand_atom_file                                             ligands_all.mol2
>ligand_outfile_prefix                                        ligands_cont_out
>limit_max_ligands                                            no
>write_orientations                                           no
>write_conformations                                          no
>initial_skip                                                 0
>calculate_rmsd                                               no
>rank_ligands                                                 yes
>max_ranked_ligands                                           500
>scored_conformer_output_override                             no
>
>Orient Ligand Parameters
>------------------------------------------------------------------------------------------
>orient_ligand                                                yes
>automated_matching                                           yes
>receptor_site_file                                           site.sph
>max_orientations                                             1000
>critical_points                                              no
>chemical_matching                                            no
>use_ligand_spheres                                           no
>
>Flexible Ligand Parameters
>------------------------------------------------------------------------------------------
>flexible_ligand                                              yes
>ag_conf_search                                               yes
>
>Anchor & Grow Parameters
>------------------------------------------------------------------------------------------
>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                                            yes
>clash_overlap                                                0.5
>
>Bump Filter Parameters
>------------------------------------------------------------------------------------------
>bump_filter                                                  yes
>bump_grid_prefix                                             grid
>max_bumps                                                    2
>
>Master Score Parameters
>------------------------------------------------------------------------------------------
>score_molecules                                              yes
>
>Energy Score Parameters
>------------------------------------------------------------------------------------------
>grid_score_primary                                           no
>grid_score_secondary                                         no
>
>Continuous Energy Score Parameters
>------------------------------------------------------------------------------------------
>continuous_score_primary                                     yes
>continuous_score_secondary                                   yes
>cont_score_rec_filename                                      r1_md_min.mol2
>cont_score_att_exp                                           6
>cont_score_rep_exp                                           12
>cont_score_dielectric                                        4
>cont_score_vdw_scale                                         1
>cont_score_es_scale                                          1
>
>Simplex Minimization Parameters
>------------------------------------------------------------------------------------------
>minimize_ligand                                              yes
>minimize_anchor                                              yes
>minimize_flexible_growth                                     yes
>minimize_final_pose                                          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_final_max_iterations                                 0
>simplex_random_seed                                          0
>
>Atom Typing Parameters
>------------------------------------------------------------------------------------------
>atom_model                                                   all
>vdw_defn_file                                                /home/starless/dock5.4/parameters/vdw_AMBER_parm99.defn
>flex_defn_file                                               /home/starless/dock5.4/parameters/flex.defn
>flex_drive_file                                              /home/starless/dock5.4/parameters/flex_drive.tbl
>chem_defn_file                                               /home/starless/dock5.4/parameters/chem.defn
>------------------------------------------------------------------------------------------
>
>Initializing Library File Routines...
>Initializing Orienting Routines...
>Initializing Conformer Generator Routines...
>Initializing Bump Filter Routines...
> Reading the bump grid from grid.bmp
>  
>
>------------------------------------------------------------------------
>
>
>
>
>--------------------------------------
>DOCK v5.4.0
>
>Released March 2006
>Copyright UCSF
>Authored by:
>	Tack Kuntz
>	Demetri Moustakas
>	Paula Therese Lang
>	Scott Pegg
>	Scott Brozell
>--------------------------------------
>
>
>Molecule Library Parameters
>------------------------------------------------------------------------------------------
>ligand_atom_file                                             ligands_all.mol2
>ligand_outfile_prefix                                        ligands_gbsa_out
>limit_max_ligands                                            no
>write_orientations                                           no
>write_conformations                                          no
>initial_skip                                                 0
>calculate_rmsd                                               no
>rank_ligands                                                 yes
>max_ranked_ligands                                           500
>scored_conformer_output_override                             no
>
>Orient Ligand Parameters
>------------------------------------------------------------------------------------------
>orient_ligand                                                yes
>automated_matching                                           yes
>receptor_site_file                                           site.sph
>max_orientations                                             1000
>critical_points                                              no
>chemical_matching                                            no
>use_ligand_spheres                                           no
>
>Flexible Ligand Parameters
>------------------------------------------------------------------------------------------
>flexible_ligand                                              yes
>ag_conf_search                                               yes
>
>Anchor & Grow Parameters
>------------------------------------------------------------------------------------------
>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                                            yes
>clash_overlap                                                0.5
>
>Bump Filter Parameters
>------------------------------------------------------------------------------------------
>bump_filter                                                  yes
>bump_grid_prefix                                             grid
>max_bumps                                                    2
>
>Master Score Parameters
>------------------------------------------------------------------------------------------
>score_molecules                                              yes
>
>Energy Score Parameters
>------------------------------------------------------------------------------------------
>grid_score_primary                                           no
>grid_score_secondary                                         no
>
>Continuous Energy Score Parameters
>------------------------------------------------------------------------------------------
>continuous_score_primary                                     no
>continuous_score_secondary                                   no
>
>Contact Score Paramters
>------------------------------------------------------------------------------------------
>contact_score_primary                                        no
>contact_score_secondary                                      no
>
>GB/SA Score Parameters
>------------------------------------------------------------------------------------------
>gbsa_pairwise_score_primary                                  yes
>gbsa_pairwise_score_secondary                                yes
>gbsa_pairwise_gb_grid_prefix                                 gb_grid
>gbsa_pairwise_sa_grid_prefix                                 sa_grid
>gbsa_pairwise_vdw_grid_prefix                                grid
>gbsa_pairwise_screen_file                                    /home/starless/dock5.4/parameters/screen.in
>gbsa_pairwise_solvent_dielectric                             78.300003
>
>Simplex Minimization Parameters
>------------------------------------------------------------------------------------------
>minimize_ligand                                              yes
>minimize_anchor                                              yes
>minimize_flexible_growth                                     yes
>minimize_final_pose                                          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_final_max_iterations                                 0
>simplex_random_seed                                          0
>
>Atom Typing Parameters
>------------------------------------------------------------------------------------------
>atom_model                                                   all
>vdw_defn_file                                                /home/starless/dock5.4/parameters/vdw_AMBER_parm99.defn
>flex_defn_file                                               /home/starless/dock5.4/parameters/flex.defn
>flex_drive_file                                              /home/starless/dock5.4/parameters/flex_drive.tbl
>chem_defn_file                                               /home/starless/dock5.4/parameters/chem.defn
>------------------------------------------------------------------------------------------
>
>Initializing Library File Routines...
>Initializing Orienting Routines...
>Initializing Conformer Generator Routines...
>Initializing Bump Filter Routines...
> Reading the bump grid from grid.bmp
>Initializing GB/SA Pairwise Score Routines...
>Initializing Energy Score Routines...
> Reading the energy grid from grid.nrg
>Ligand on receptor inva error: 97	-0.140729
>Ligand on receptor inva error: 97	-0.175361
>Ligand on receptor inva error: 97	-0.158546
>Ligand on receptor inva error: 97	-0.101178
>Ligand on receptor inva error: 97	-0.0121233
>Receptor on ligand inv_a error: 9	-0.408357
>Receptor on ligand inv_a error: 10	-0.687585
>Receptor on ligand inv_a error: 14	-0.502356
>Receptor on ligand inv_a error: 9	-0.12934
>Receptor on ligand inv_a error: 10	-0.578806
>Receptor on ligand inv_a error: 9	-0.844391
>Receptor on ligand inv_a error: 10	-1.27744
>Receptor on ligand inv_a error: 10	-0.223413
>Receptor on ligand inv_a error: 13	-0.0821992
>Receptor on ligand inv_a error: 10	-0.139229
>Receptor on ligand inv_a error: 13	-0.178968
>Receptor on ligand inv_a error: 13	-0.18605
>Receptor on ligand inv_a error: 10	-0.213326
>Receptor on ligand inv_a error: 13	-0.148797
>Receptor on ligand inv_a error: 13	-0.00336685
>Receptor on ligand inv_a error: 13	-0.229898
>Receptor on ligand inv_a error: 13	-0.221723
>Receptor on ligand inv_a error: 13	-0.154793
>Receptor on ligand inv_a error: 13	-0.356406
>Receptor on ligand inv_a error: 13	-0.44132
>Receptor on ligand inv_a error: 9	-0.920063
>Receptor on ligand inv_a error: 10	-0.557254
>Receptor on ligand inv_a error: 13	-0.217702
>Receptor on ligand inv_a error: 13	-0.950965
>Ligand on receptor inva error: 61	-0.111157
>Receptor on ligand inv_a error: 13	-0.209255
>Receptor on ligand inv_a error: 13	-0.281936
>Receptor on ligand inv_a error: 13	-0.116654
>Receptor on ligand inv_a error: 13	-0.244925
>Receptor on ligand inv_a error: 10	-0.0377023
>Receptor on ligand inv_a error: 13	-0.00350275
>Receptor on ligand inv_a error: 10	-0.127165
>Receptor on ligand inv_a error: 13	-0.0270678
>Receptor on ligand inv_a error: 13	-0.250024
>Receptor on ligand inv_a error: 13	-0.225254
>Receptor on ligand inv_a error: 13	-0.149016
>Receptor on ligand inv_a error: 10	-0.00634315
>Receptor on ligand inv_a error: 13	-0.0755811
>Receptor on ligand inv_a error: 13	-0.110082
>Receptor on ligand inv_a error: 13	-0.063265
>Receptor on ligand inv_a error: 13	-0.0575069
>Receptor on ligand inv_a error: 13	-0.128243
>Receptor on ligand inv_a error: 10	-0.155796
>Receptor on ligand inv_a error: 10	-0.163929
>Receptor on ligand inv_a error: 10	-0.212521
>Receptor on ligand inv_a error: 13	-0.0121241
>Receptor on ligand inv_a error: 13	-0.0819321
>Receptor on ligand inv_a error: 10	-0.0745338
>Receptor on ligand inv_a error: 10	-0.0929771
>Receptor on ligand inv_a error: 10	-0.0679001
>Receptor on ligand inv_a error: 13	-0.0182923
>Receptor on ligand inv_a error: 10	-0.000462201
>Receptor on ligand inv_a error: 10	-0.0210213
>Receptor on ligand inv_a error: 10	-0.0147331
>Receptor on ligand inv_a error: 10	-0.0102747
>Receptor on ligand inv_a error: 10	-0.00479641
>Receptor on ligand inv_a error: 10	-0.00422528
>Receptor on ligand inv_a error: 10	-0.0230261
>Receptor on ligand inv_a error: 10	-0.000128415
>Receptor on ligand inv_a error: 10	-0.0011076
>Receptor on ligand inv_a error: 10	-0.00452187
>Receptor on ligand inv_a error: 10	-0.00811341
>Receptor on ligand inv_a error: 10	-0.00115695
>Receptor on ligand inv_a error: 10	-0.00132063
>Receptor on ligand inv_a error: 10	-0.00336495
>Receptor on ligand inv_a error: 10	-0.00584307
>Receptor on ligand inv_a error: 10	-0.0024431
>Receptor on ligand inv_a error: 10	-0.00105801
>Receptor on ligand inv_a error: 10	-0.00135699
>Receptor on ligand inv_a error: 10	-0.00319102
>Receptor on ligand inv_a error: 9	-1.35048
>Receptor on ligand inv_a error: 10	-0.575054
>Receptor on ligand inv_a error: 13	-0.0849022
>Receptor on ligand inv_a error: 14	-0.279756
>Ligand on receptor inva error: 97	-0.0743039
>Ligand on receptor inva error: 99	-0.331121
>Receptor on ligand inv_a error: 13	-0.116846
>Receptor on ligand inv_a error: 14	-0.250138
>Ligand on receptor inva error: 40	-0.139178
>Ligand on receptor inva error: 96	-0.0607544
>Ligand on receptor inva error: 99	-0.399506
>Ligand on receptor inva error: 100	-0.140247
>Ligand on receptor inva error: 111	-0.0182245
>Receptor on ligand inv_a error: 9	-0.475418
>Receptor on ligand inv_a error: 13	-0.291441
>Receptor on ligand inv_a error: 14	-0.766972
>Ligand on receptor inva error: 40	-0.0476437
>Ligand on receptor inva error: 99	-0.445644
>Receptor on ligand inv_a error: 9	-0.89799
>Receptor on ligand inv_a error: 10	-0.403999
>Receptor on ligand inv_a error: 13	-0.0182302
>Receptor on ligand inv_a error: 14	-0.532694
>Ligand on receptor inva error: 99	-0.448526
>Receptor on ligand inv_a error: 10	-0.176982
>Ligand on receptor inva error: 40	-0.0373851
>Receptor on ligand inv_a error: 13	-0.584492
>Receptor on ligand inv_a error: 14	-0.749008
>Ligand on receptor inva error: 99	-0.284517
>Ligand on receptor inva error: 100	-0.305746
>Receptor on ligand inv_a error: 13	-0.66889
>Receptor on ligand inv_a error: 14	-1.10783
>Ligand on receptor inva error: 40	-0.0142971
>Ligand on receptor inva error: 99	-0.434283
>Ligand on receptor inva error: 100	-0.215873
>Receptor on ligand inv_a error: 13	-0.330215
>Receptor on ligand inv_a error: 14	-0.31177
>Ligand on receptor inva error: 40	-0.192885
>Ligand on receptor inva error: 99	-0.250302
>Ligand on receptor inva error: 100	-0.0887325
>Receptor on ligand inv_a error: 9	-0.752404
>Receptor on ligand inv_a error: 10	-0.232343
>Receptor on ligand inv_a error: 13	-0.104506
>Receptor on ligand inv_a error: 14	-0.567083
>Ligand on receptor inva error: 40	-0.00441408
>Ligand on receptor inva error: 99	-0.838665
>Receptor on ligand inv_a error: 9	-1.59077
>  
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Dock-fans mailing list
>Dock-fans at docking.org
>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





More information about the Dock-fans mailing list