[Dock-fans] secondary score conformers mol2 file

wei wang pharma at whu.edu.cn
Tue Jul 30 09:33:19 PDT 2013


Hi everyone,

 

I'm trying to rescore the small molecule database using the Hawkins GB/SA
scoring function. Both primary and secondary score results in .out file are
good. Everything looks fine except there is no useful secondary score
conformers mol2 files (In fact, there is zero size file named with
secondary_scored.mol2).  We can check the primary conformer mol2 without
problem. So how can we get the secondary score conformers mol2 files.

Thanks  a lot.

 

Here is attached my in file

ligand_atom_file
rigid.out_scored.mol2

limit_max_ligands                                            no

skip_molecule                                                no

read_mol_solvation                                           no

calculate_rmsd                                               no

use_database_filter                                          no

orient_ligand                                                no

use_internal_energy                                          no 

flexible_ligand                                              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

multigrid_score_secondary                                    no

dock3.5_score_secondary                                      no

continuous_score_secondary                                   no

descriptor_score_secondary                                   no

gbsa_zou_score_secondary                                     no

gbsa_hawkins_score_secondary                                 yes 

gbsa_hawkins_score_rec_filename                              HT.mol2

gbsa_hawkins_score_solvent_dielectric                        78.5

gbsa_hawkins_use_salt_screen                                 yes

gbsa_hawkins_score_salt_conc(M)                              0.15

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                               9

minimize_ligand                                              no

simplex_max_iterations                                       1

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                    no

simplex_secondary_max_iterations                             1

simplex_random_seed                                          0

simplex_restraint_min                                        no

atom_model                                                   all

vdw_defn_file
/dawnfs/software/dock6/parameters/vdw_AMBER_parm99.defn

flex_defn_file
/dawnfs/software/dock6/parameters/flex.defn

flex_drive_file
/dawnfs/software/dock6/parameters/flex_drive.tbl

ligand_outfile_prefix                                        h_gbsa

write_orientations                                           no

num_primary_scored_conformers_rescored                       1

num_secondary_scored_conformers                              1

rank_primary_ligands                                         no

rank_secondary_ligands                                       no

 

Sincerely 

Wei Wang

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