[Dock-fans] About the error of docking

Scott Brozell sbrozell at scripps.edu
Tue Sep 18 09:05:21 PDT 2007


Hi,

On Tue, 18 Sep 2007, Sudipto Mukherjee wrote:

> Dock appear to be taking about 12 hours for each molecule. This is definitely not normal.
> Could you provide details about what kind of molecules you are docking in?
> Dock is designed to work only with small molecules, and works best with those having 7 or fewer rotatable bonds.

> On Tue, 18 Sep 2007, wang wrote:
>
> > When I ran dock 6.1 to screen a database , the error happened . The
> > error message is
> > shown below. Could you tell me how to fix the problem ?

Did you try the suggested recovery emitted after the first error ?

As the error message and Sudipto suggest, your molecules are
probably too big.

Scott

> >
> > Error
> > __________________________________________________________________________
> > ...........
> >
> > Initializing Library File Routines...
> > Initializing Orienting Routines...
> > Initializing Conformer Generator Routines...
> > Initializing Grid Score Routines...
> > Reading the energy grid from ./grid.nrg
> > Error: memory exhausted!
> > For Unix platforms increase the datasize, stacksize, and
> > memoryuse using the limit, ulimit, or unlimit commands.
> >
> > -----------------------------------
> > Molecule: 005
> >
> > Elapsed time: 41596 seconds
> >
> > ERROR: Could not complete growth.
> > Confirm grid box is large enough to contain
> > ligand and try increasing max_orients.
> >
> > -----------------------------------
> > Molecule: 006
> >
> > Elapsed time: 41723 seconds
> >
> > ERROR: Could not complete growth.
> > Confirm grid box is large enough to contain
> > ligand and try increasing max_orients.
> >
> >
> >
> > .................
> >
> >
> >
> > dock.in
> > ___________________________________________________________________________
> >
> > ligand_atom_file ./dy1modif.mol2
> > limit_max_ligands no
> > skip_molecule no
> > read_mol_solvation no
> > calculate_rmsd yes
> > use_rmsd_reference_mol yes
> > rmsd_reference_filename ./dy1modif.mol2
> > orient_ligand yes
> > automated_matching yes
> > receptor_site_file ./selected_spheres.sph
> > max_orientations 100
> > critical_points no
> > chemical_matching no
> > use_ligand_spheres no
> > flexible_ligand yes
> > min_anchor_size 50
> > pruning_use_clustering yes
> > pruning_max_orients 500
> > 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 no
> > score_molecules yes
> > contact_score_primary no
> > contact_score_secondary no
> > grid_score_primary yes
> > grid_score_secondary yes
> > grid_score_rep_rad_scale 1
> > grid_score_vdw_scale 1
> > grid_score_es_scale 1
> > grid_score_grid_prefix ./grid
> > minimize_ligand yes
> > minimize_anchor no
> > 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_grow_max_iterations 10
> > simplex_final_min no
> > simplex_secondary_minimize_pose no
> > simplex_random_seed 0
> > atom_model all
> > vdw_defn_file ../dock6/parameters/vdw_AMBER_parm99.defn
> > flex_defn_file ../dock6/parameters/flex.defn
> > flex_drive_file ../dock6/parameters/flex_drive.tbl
> > ligand_outfile_prefix rpr
> > write_orientations yes
> > num_primary_scored_conformers_rescored 1
> > num_secondary_scored_conformers_written 1
> > rank_primary_ligands no
> > rank_secondary_ligands no
> >


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