[Dock-fans] empty output files

Sebastien Gerega sger3477 at mail.usyd.edu.au
Thu Apr 28 18:58:19 PDT 2005

I want to use DOCK to fine the best conformation when a ligand is bound to
a protein. I am not searching a database, I just want to know the best
conformation. I believe I am doing everything correctly and I get no
errors but all the output files are completely empty, 0kb.

Any suggestions what I could be doing wrong?

These are the parameters for my DOCK run:

ligand_atom_file                                             chaina.mol2
ligand_outfile_prefix                                        output
limit_max_ligands                                            no
write_orientations                                           yes
write_conformations                                          yes
initial_skip                                                 0
calculate_rmsd                                               no
rank_ligands                                                 yes
max_ranked_ligands                                           500
scored_mol_output_override                                   no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           chainb.pdb.sph
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           yes
ligand_sphere_file                                           chaina.pdb.sph
flexible_ligand                                              yes
ag_conf_search                                               yes
min_anchor_size                                              50
num_anchor_poses                                             50
number_confs_per_cycle                                       50
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                                             gridIn
max_bumps                                                    2
score_molecules                                              yes
energy_score_primary                                         yes
energy_score_secondary                                       yes
vdw_scale                                                    1
es_scale                                                     1
nrg_grid_prefix                                              gridIn
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
minimize_final_pose                                          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_min_max_iterations                            50
simplex_flex_min_max_iterations                              10
simplex_final_min_max_iterations                             100
simplex_random_seed                                          0
atom_model                                                   all
vdw_defn_file                                                vdw.defn
flex_defn_file                                               flex.defn
flex_drive_file                                              flex_drive.tbl
chem_defn_file                                               chem.defn
num_scored_poses_written                                     1

Sebastien Gerega

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