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dock6.mpi -i dock6-em.in
Initializing MPI Routines...

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DOCK v6.9

Released November 2018
Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

ligand_atom_file 3D5X-ligand.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd yes
use_rmsd_reference_mol yes
rmsd_reference_filename 3D5X-ligand.mol2

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand yes
automated_matching yes
receptor_site_file receptor.sph
max_orientations 1000
critical_points yes
chemical_matching yes
chem_match_tbl /home/lab/dock6/parameters/chem_match.tbl
use_ligand_spheres no

Bump Filter Parameters

bump_filter yes
bump_grid_prefix grid
max_bumps_anchor 2
max_bumps_growth 2

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary yes
contact_score_secondary yes
contact_score_cutoff_distance 3.5
contact_score_clash_overlap 0.75
contact_score_clash_penalty 50
contact_score_grid_prefix grid

Simplex Minimization Parameters

minimize_ligand yes
simplex_max_iterations 1000
simplex_tors_premin_iterations 0
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_secondary_minimize_pose yes
use_advanced_secondary_simplex_parameters yes
simplex_secondary_max_iterations 100
simplex_secondary_max_cycles 1
simplex_secondary_score_converge 0.1
simplex_secondary_cycle_converge 1.0
simplex_secondary_trans_step 1.0
simplex_secondary_rot_step 0.1
simplex_secondary_tors_step 10.0
simplex_random_seed 0
simplex_restraint_min yes
simplex_coefficient_restraint 10.0

Atom Typing Parameters

atom_model all
vdw_defn_file /home/lab/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file /home/lab/dock6/parameters/flex.defn
flex_drive_file /home/lab/dock6/parameters/flex_drive.tbl
chem_defn_file /home/lab/dock6/parameters/chem.defn

Molecule Library Output Parameters

ligand_outfile_prefix 3D5X.lig.min
write_orientations no
num_primary_scored_conformers_rescored 10
write_primary_conformations yes
cluster_primary_conformations yes
cluster_rmsd_threshold 2.0
num_clusterheads_for_rescore 5
num_secondary_scored_conformers 10
write_secondary_conformations yes
rank_primary_ligands yes
max_primary_ranked 500
rank_secondary_ligands yes
max_secondary_ranked 500

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Bump Filter Routines...
Reading the bump grid from grid.bmp
Done reading the bump grid.
Initializing Contact Score Routines...
Reading the contact grid from grid.cnt
Done reading the contact grid.
Reading the grid box quantifiers from grid.bmp
Done reading the grid box quantifiers.
Segmentation fault (core dumped)