[Dock-fans] dock 6.1 and 6.2

[Scott Brozell]

Hi,

There are no intentional changes to pose generation in 6.2:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-March/001433.html

Can you confirm that everything besides the version change is the same:
machine, compilers, grid, etc ?

Scott

On Fri, 21 Mar 2008, Yunierkis Perez Castillo wrote:

> Hi all, i have been trying dock 6.2 using the same parameters I have
> used before with dock 6.1 and the results I'm obtaining are very
> different.
> I'm trying to dock various different inhibitors to an enzyme, with 6.1 I
> can't find a valid binding pose for many ligands to the receptor, which
> seems reasonable because conformational changes are required to
> accommodate certain ligands in the binding site.
> On the other hand, 6.2 can find  a "valid" binding pose for all the
> ligands, the problem is that must of this binding poses show many
> internal bumps and are totally unreasonable. My experience with 6.1
> indicates that binding poses generated using this version are of good
> quality.
> Below is my parameters file. Is there any mistake on it???
> 
> 
> ligand_atom_file
> ligands.mol2
> limit_max_ligands                                            no
> skip_molecule                                                no
> read_mol_solvation                                           no
> calculate_rmsd                                               no
> orient_ligand                                                yes
> automated_matching                                           yes
> receptor_site_file                                           ../receptor/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                                          25
> pruning_clustering_cutoff                                    25
> use_internal_energy                                          yes
> internal_energy_att_exp                                      6
> internal_energy_rep_exp                                      12
> internal_energy_dielectric                                   4.0
> use_clash_overlap                                            yes
> clash_overlap                                                0.5
> bump_filter                                                  yes
> bump_grid_prefix                                             ../grid/grid
> max_bumps_anchor                                             2
> max_bumps_growth                                             2
> 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/grid
> 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                                           25
> 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                                50
> simplex_grow_max_iterations                                  50
> simplex_final_min                                            yes
> simplex_final_min_rep_rad_scale                              1
> simplex_final_min_add_internal                               yes
> simplex_final_max_iterations                                 50
> simplex_random_seed                                          0
> atom_model                                                   all
> vdw_defn_file                                                /gfs/progs/Docking/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file                                               /gfs/progs/Docking/dock6/parameters/flex.defn
> flex_drive_file                                              /gfs/progs/Docking/dock6/parameters/flex_drive.tbl
> ligand_outfile_prefix                                        output
> write_orientations                                           no
> num_scored_conformers                                        1
> rank_ligands                                                 no