[Dock-fans] re "Could not complete growth" error from Dock v. 6.2

Vidana.Epa at csiro.au Vidana.Epa at csiro.au
Mon May 11 17:53:38 PDT 2009


Hi Dock fans,

            I am flexible ligand docking (Dock v.6.2) a database to a site in a protein, and I notice some molecules fail to dock with the error message:
"Could not complete growth. Confirm that the grid box is large enough to contain the ligand and try increasing max_orientations." For a failed molecule that I looked at the grid box is certainly large enough. For this molecule, I had to increase max_orientations all the way up to 50000 (!) before it finally docked successfully. I am not sure whether this is the right remedy for the problem. (When it fails, I am not sure why the "c_library.num_confs" is zero; unfortunately, being a fortran and not a c++ person, I am hampered in delving too deeply into the source code). I noticed this problem was raised a few months ago by Jim Parker in the mail archives, and I don't know if a satisfactory solution was found. Can anyone shed some light on this problem? (f.y.i, I've appended the dock.in to this.)

Thanks very much.

Cheers,

Vidana.


ligand_atom_file                                             sub100_t13_76.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       yes
rmsd_reference_filename                                      sub100_t13_76.mol2
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           sphgen_cluster1_final.sph
max_orientations                                             10000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              yes
min_anchor_size                                              40
pruning_use_clustering                                       yes
pruning_max_orients                                          100
pruning_clustering_cutoff                                    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                                             grid_r10
max_bumps_anchor                                             2
max_bumps_growth                                             2
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                                       grid_r10
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_final_min                                            no
simplex_random_seed                                          0
atom_model                                                   all
vdw_defn_file                                                /software/dock6.2/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /software/dock6.2/parameters/flex.defn
flex_drive_file                                              /software/dock6.2/parameters/flex_drive.tbl
ligand_outfile_prefix                                        sub100_t13_76_7
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no



Vidana C. Epa

CSIRO,
Division of Molecular Health & Technologies,
343 Royal Parade,
Parkville, Victoria 3052,
AUSTRALIA.

tel: (61) - 3 - 9662 - 7345
fax:(61) - 3 - 9662 - 7347

email: Vidana.Epa at csiro.au

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