[Dock-fans] dock 6.1 and 6.2

[Scott Brozell]

Hi,

Thanks for double checking.
Can you send me all the necessary input files ?

thanks,
Scott

On Mon, 24 Mar 2008, Yunierkis Perez Castillo wrote:

> I have recompiled dock 6.1 and 6.2 again in the same computer and the
> results are the same.
> It seems like 6.2 don't consider the internal energy of the ligand
> during the grow process and then conformations with internal clashes are
> not discarded.
> Below are two pictures of dock results. The first show one ligand after
> docking with 6.1 (cyan) and 6.2 (colored by atom), The results from 6.2
> show clashes between one of the chlorine substituent of the ring and the
> central part of the molecule. The other image shows a ligand that can't
> be docked by 6.1 but by 6.2 with a lot of internal clashes.
> 
> On Sat, 2008-03-22 at 12:40 -0800, Scott Brozell wrote:
> 
> > 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
> >