[Dock-fans] About the error of docking

wang c00jsw00 at nchc.org.tw
Mon Sep 17 20:10:42 PDT 2007


Dear all ,
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 ?
Thanks

Wang


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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