[Dock-fans] secondary score conformers mol2 file

William Joseph Allen william.joseph.allen at gmail.com
Tue Jul 30 10:03:44 PDT 2013


Hi Wei Wang,

My understanding is that the score_secondary functions are not very
reliable. You may have more success if you perform two consecutive
re-scores: in the first re-score set grid_score_primary = yes, then in the
second re-score set gbsa_hawkins_score_primary = yes. This is generally how
we do it in our group.

Joe Allen


On Tue, Jul 30, 2013 at 12:33 PM, wei wang <pharma at whu.edu.cn> wrote:

> 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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>
>


-- 
William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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