[Dock-fans] critical points and automated matching

Terry Lang terry at cgl.ucsf.edu
Wed Oct 11 15:20:28 PDT 2006


Dear Anna,

>
>   From DOCK4 manual i found that if you use critical points you have to
> set a manual matching run instead of automated matching. Is it correct?

You can run critical points with automated matching in DOCK 5 and DOCK 6.

>
> First_
> Using cluster.sph file for spheres
>
> _I run critical points + manual matching and dock exit with a
> segmentation fault error.
>
We have found problems in the past with manual matching.  Try running 
with automatic matching to see if your problem is resolved.  We have put 
this problem on the bug fix list for DOCK 6 and will post a solution on 
the bug fix page.  However, we no longer support DOCK 5.4.

> I run the same calculation with critical points + automated matching and
> it finish correctly but form the orientation scored it doesn't seem that
> any critical point has been considered because the fragment is away from
> those spheres.
>
> How should i consider this last result with automated matching?
>
The final conformations for the critical matching may indeed be some 
distance away from the critical points if you are minimizing during your 
run depending on whether the molecules can fit in the area of the active 
site you have defined as critical.

> Second
> Is it the definition of critical points in cluster.sph file correct, or
> should I give different names to each of the critical point? (i.e.
> sphere 795...1, sphere 804...2..)

This definition is probably not correct for your purposes.  If you are 
trying to hit a section of the active site, you should label all the 
spheres in that section by the same number.  The labeling method you are 
using now will match either sphere 795 or sphere 2 as being critical.  
For more information on labeling spheres, go to the DOCK 6 manual on our 
web site at dock.compbio.ucsf.edu under Sphgen >> Output.

Sincerely,
Terry

> Thank you for your help
> Anna
>
>------------------------------------------------------------------------
>
>ligand_atom_file                                             framm_h.mol2
>ligand_outfile_prefix                                        fr_critical
>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                             yes
>num_scored_conformers_written                                5
>cluster_conformations                                        yes
>cluster_rmsd_threshold                                       2.0
>orient_ligand                                                yes
>automated_matching                                           no
>distance_tolerence                                           0.25
>distance_minimum                                             2.0
>nodes_minimum                                                3
>nodes_maximum                                                10
>receptor_site_file                                           critical.sph
>max_orientations                                             2500
>critical_points                                              no
>chemical_matching                                            no
>use_ligand_spheres                                           no
>flexible_ligand                                              yes
>ag_conf_search                                               yes
>min_anchor_size                                              5
>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                                            no
>bump_filter                                                  yes
>bump_grid_prefix                                             rec_h1
>max_bumps                                                    4
>score_molecules                                              yes
>grid_score_primary                                           yes
>grid_score_secondary                                         no
>grid_score_vdw_scale                                         1
>grid_score_es_scale                                          1
>grid_score_grid_prefix                                       rec_h1
>continuous_score_secondary                                   no
>contact_score_secondary                                      yes
>contact_score_cutoff_distance                                4.5
>contact_score_clash_overlap                                  0.75
>contact_score_clash_penalty                                  50
>contact_score_grid_prefix                                    rec_h1
>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                                 1000
>simplex_random_seed                                          0
>atom_model                                                   all
>vdw_defn_file                                                /xyz/SW/dock.5.4.0_sgi/parameters/vdw_AMBER_parm99.defn
>flex_defn_file                                               /xyz/SW/dock.5.4.0_sgi/parameters/flex.defn
>flex_drive_file                                              /xyz/SW/dock.5.4.0_sgi/parameters/flex_drive.tbl
>chem_defn_file                                               /xyz/SW/dock.5.4.0_sgi/parameters/chem.defn
>gbsa_pairwise_score_secondary                                no
>
>
>  
>
>------------------------------------------------------------------------
>
>DOCK 3.5 receptor_spheres
>cluster     1   number of spheres in cluster    52
>  180   5.91036  -8.70557  13.83769   2.828  833 0  0
>  187   8.08679 -10.86944  16.58072   1.751  235 0  0
>  198   8.85151 -10.44059  15.75947   2.446  235 0  0
>  200  11.10110 -10.46015  17.93329   1.603  217 0  0
>  214  22.82801  -8.90580  16.60071   2.611  464 0  0
>  216  13.66460  -9.07152  14.37946   3.079 1177 0  0
>  217  10.47601 -10.07496  17.73323   2.056  199 0  0
>  218  10.76914  -9.20500  16.90092   2.729  199 0  0
>  222   9.52073 -10.11779  17.80582   1.857  235 0  0
>  233   5.46875 -10.13150  15.64188   1.482  186 0  0
>  234   5.73307  -7.24841  14.07930   2.826  833 0  0
>  334   3.02610  -4.90006  14.76884   2.443 1213 0  0
>  335   4.93174  -3.50410  19.91751   1.795  783 0  0
>  336   4.57537  -2.63940  20.97961   1.400  782 0  0
>  347   6.71049  -4.11858  18.58484   2.055  784 0  0
>  350   8.31828  -3.71106  17.52455   2.514  784 0  0
>  351  10.05604  -5.30482  16.37742   2.696 1294 0  0
>  366  14.52686  -5.52368  22.09254   2.254  459 0  0
>  368  14.45111  -5.37706  22.00669   2.280  459 0  0
>  459  14.42946  -5.41780  21.77542   2.248  351 0  0
>  462  14.43664  -5.44458  19.45154   2.145  351 0  0
>  466  14.40843  -5.08725  21.78625   2.190  351 0  0
>  498   9.41157  -2.97858  17.34690   2.332 1288 0  0
>  499  10.11148  -3.43298  16.87200   2.221 1289 0  0
>  500   8.46903  -2.06600  20.62379   1.635  767 0  0
>  766   6.77936  -2.61064  21.10697   1.583  783 0  0
>  767   8.26177  -2.22658  20.73279   1.588  350 0  0
>  771   5.14289  -3.11736  20.74156   1.759  783 0  0
>  782   5.10639  -2.87119  20.91517   1.571  771 0  0
>  783   8.72541  -3.32517  17.42162   2.530 1289 0  0
>  784   8.07419  -4.01062  17.34649   2.595  349 0  0
>  785   9.12459  -2.72893  17.91144   2.119  498 0  0
>  795   3.01384  -1.17348  16.04457   1.612 1214 1  0
>  804   1.54438  -3.19458  15.17832   1.484  334 1  0
>  806   2.26515  -3.32882  15.03769   1.736  334 0  0
>  807   2.61209  -1.93437  15.61482   1.698  334 0  0
>  811   2.98079  -5.37147  14.53182   2.593 1213 0  0
>  822   2.17378  -6.87135  12.64234   2.226  180 0  0
>  826   2.73506  -6.39624  13.00602   2.499  180 0  0
>  827   2.74827  -4.73607  12.46960   1.706 1213 0  0
>  831   7.25687  -9.48944  10.01141   1.617 1189 0  0
> 1212   2.80670  -4.64528  14.60241   2.280  811 0  0
> 1213   6.87589  -6.96481  14.10834   2.912  235 0  0
> 1214   3.95528  -2.99258  16.00604   1.813  334 0  0
> 1288   9.13693  -3.05812  17.43920   2.418  351 0  0
> 1290  10.30653  -2.91520  16.97134   1.903  499 0  0
> 1291  10.02506  -2.05728  17.56847   1.564  498 0  0
> 1297  13.63111  -5.88471  18.35494   2.041  351 0  0
> 1312  15.23881  -3.84501  19.58256   1.605  499 0  0
> 1212   2.80670  -4.64528  14.60241   2.280  811 0  0
> 1213   6.87589  -6.96481  14.10834   2.912  235 0  0
> 1214   3.95528  -2.99258  16.00604   1.813  334 0  0
>
>
>  
>
>------------------------------------------------------------------------
>
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>  
>

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

 




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