[Dock-fans] Scoring and parallel processing problems

Dmitry Osolodkin divanych at rambler.ru
Tue May 2 09:23:32 PDT 2006


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
-------------- next part --------------



--------------------------------------
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
-------------- next part --------------



--------------------------------------
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


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