[Dock-fans] Help: a question about gbsa_hawkins_score_primary

[thirsty]

I have written "gbsa_hawkins_score_primary  yes" in dock.in

when i run dock6, "gbsa_hawkins_score_primary  yes" was deleted, Why?

Thank you!!

GuanXin
2009.03.18

"ligand_atom_file
inno-406_ligand.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file
selected_spheres.sph
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              yes
min_anchor_size                                              8
pruning_use_clustering                                       yes
pruning_max_orients                                          100
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                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 yes
gbsa_hawkins_score_rec_filename                              inno406.mol2
gbsa_hawkins_score_solvent_dielectric                        78.5
gbsa_hawkins_use_salt_screen                                 no
gbsa_hawkins_score_gb_offset                                 0.09
gbsa_hawkins_score_cont_vdw_and_es                           yes
gbsa_hawkins_score_vdw_att_exp                               6
gbsa_hawkins_score_vdw_rep_exp                               12
grid_score_rep_rad_scale                                     1
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           2
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_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_final_min                                            no
simplex_secondary_minimize_pose                              yes
use_advanced_secondary_simplex_parameters                    no
simplex_secondary_max_iterations                             100
simplex_secondary_min_add_internal                           no
simplex_random_seed                                          1
atom_model                                                   all
vdw_defn_file                                                vdw.defn
flex_defn_file                                               flex.defn
flex_drive_file                                              flex_drive.tbl
ligand_outfile_prefix                                        GBSA
write_orientations                                           no
num_primary_scored_conformers_rescored                       1
num_secondary_scored_conformers_written                      1
rank_primary_ligands                                         no
rank_secondary_ligands                                       no
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