[Dock-fans] About the error of docking

Sudipto Mukherjee sudmukh at yahoo.com
Tue Sep 18 08:38:20 PDT 2007


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.
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744

----- Original Message ----
From: wang <c00jsw00 at nchc.org.tw>
To: dock-fans at docking.org
Sent: Monday, September 17, 2007 11:10:42 PM
Subject: [Dock-fans] About the error of docking

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 ?



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.



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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