[Dock-fans] docking resukt problem!!!

"천광우" zeuschem at skku.edu
Wed Aug 10 23:04:57 PDT 2005


hello. I,m biochemist.
my first docking result  has aproblem. docked regand conformation is unstablehindrance.(bumping and large steric hindrance)
tell me, my mistake. 
my dock.in file is below.

---------------------------------------------------
ligand_atom_file                                           lig-124.mol2
ligand_outfile_prefix                                        lig
limit_max_ligands                                            no
write_orientations                                           no
write_conformations                                          no
initial_skip                                                 0
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no
rank_ligands                                                 no
num_scored_poses_written                                     1
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                          selected_spheres.sph
max_orientations                                             10000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              yes
ag_conf_search                                               yes
min_anchor_size                                              10
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                                             grid
max_bumps                                                    0
score_molecules                                              yes
energy_score_primary                                         yes
energy_score_secondary                                       yes
vdw_scale                                                    1
es_scale                                                     1
nrg_grid_prefix                                              grid
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                                                /usr/local/dock.5.2_linux/parameters/vdw_AMBER_parm96.defn
flex_defn_file                                               /usr/local/dock.5.2_linux/parameters/flex.defn
flex_drive_file                                              /usr/local/dock.5.2_linux/parameters/flex_drive.tbl
chem_defn_file                                               /usr/local/dock.5.2_linux/parameters/chem.defn
max_ranked_ligands                                           10
scored_mol_output_override                                   no
contact_cutoff_distance                                      0
---------------------------------------------------
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