[Dock-fans] dock 6.1 and 6.2

[Ben Keshet]

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?
To: dock-fans at docking.org
Message-ID:
	<daa6d6230803192346o5e213801h78702de9f4559d6f at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all:

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??

Thank for u help!!

GuanXin
2008.03.20

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
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