[Dock-fans] critical points and automated matching

anna ferrari annafarm.ferrari at unimore.it
Wed Oct 4 00:44:30 PDT 2006


Dear all
I'm docking a small fragment using Dock5.4 version defining some
critical points into my spheres cluster.
   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?
I run differen cases and this is what i had


First_
Using cluster.sph file for spheres

_I run critical points + manual matching and dock exit with a
segmentation fault error.

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?
What version of DOCK is able to correctly calculate orintations with
critical point option?

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..)


Thank you for your help
Anna

-- 
******************************************************************
Anna M. Ferrari
Dip.Scienze Farmaceutiche              Ph. +39.059.205.5122
Universita' di Modena e Reggio Emilia  Fax +39.059.205.5131
Via G. Campi 183                       annafarm.ferrari at unimore.it
41100 Modena Italy

******************************************************************



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


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