[Dock-fans] Help:why the es of grid score = 0.0000?

[Scott Brozell]

Hi,

I agree that the charges are most likely the problem.

Scott

On Fri, 21 Mar 2008, Ben Keshet wrote:

> GuanXin,
> 
> I am not a dock expert, but I can contribute few comments.  First, the Grid score is the total of the vdw and es, so it is not surprising that when you have es=0 the total score is only the vdw contribution.  I am not sure why you are getting sometimes es=0 (how are you adding charges and hydrogens? what is the difference in the docked pose between the two runs?).  
> 
> Otherwise, I think few things in your input file may lead to poor output: 
> min_anchor_size=40 is pretty big, depands on how your ligand looks like you may want to lower this value (6-10).  Additionally, I would increase your minimization parameters such as simplex_max_cycles and random_seed and observe their effect on the final pose.  
> 
> Good luck,
> Ben 
> 
> Date: Thu, 20 Mar 2008 14:46:19 +0800
> From: thirsty <thirstymail at gmail.com>
> Subject: [Dock-fans] Help:why the es of grid score = 0.0000?
> 
> I make some molecules dock to protein, the result is
> 
> grid score:
>          vdw:
>            es:
> 
> but sometime, the es=0.0000   vdw = grid score
> 
>  Grid Score:          -59.719940
>            vdw:          -59.719940
>             es:            0.000000
> 
> generally,  the results of grid score/vdw/es are different each other.
> 
> Grid Score:          -81.593117
> vdw:          -66.652908
> es:          -14.940211
> 
> I use the same dock.in file, but the result is different, why??
> 
> the following is my dock.in
> 
> ligand_atom_file                                             a.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                                              40
> 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-ch3
> dock3.5_score_secondary                                      no
> continuous_score_secondary                                   no
> gbsa_zou_score_secondary                                     no
> gbsa_hawkins_score_secondary                                 no
> amber_score_secondary                                        no
> minimize_ligand                                              yes
> minimize_anchor                                              yes
> minimize_flexible_growth                                     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_max_iterations                                500
> simplex_grow_max_iterations                                  500
> simplex_final_min                                            no
> simplex_random_seed                                          0
> atom_model                                                   all
> vdw_defn_file                                                vdw.defn
> flex_defn_file                                               flex.defn
> flex_drive_file                                              flex_drive.tbl
> ligand_outfile_prefix                                        e1
> write_orientations                                           no
> num_scored_conformers_written                                1
> rank_ligands                                                 no