Testset Protocols

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Rigid Docking Baseline Input

Ligand torsions are not sampled. The whole ligand is treated as the anchor and matched to the spheres. 0.3A grids are used with am1bcc charges on the ligand. amber99 charges and vdw parameters are used for everything else. If rank ligands are set to 'yes', dock does not report a cluster size. The number of simplex_max_iterations improves minimization while adding minimally to the runtime on the grid.

Fixed Anchor Docking Baseline

Anchor orientation is disabled. Instead, the ligand is minimized on the receptor coordinates (ligand.xtm.mol2). The largest anchor recovered is used for flexible growth. A clash overlap of 0.5 is used to avoid poor ligand conformations.

Flexible Docking Baseline

Flexible ligand docking where the largest anchor is oriented is matched to the spheres. Each anchor orient is grown along the torsions to generate poses.

On mathlab computers this binary is located at /home/sudipto/dock6/dock6_09-02-18/bin/dock6

Complete Input files for DOCK6 09-02-18

Rigid Docking Flexible Docking
ligand_atom_file                 ligand.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               spheres.sph
max_orientations                 1000
critical_points                  no
chemical_matching                no
use_ligand_spheres               no
use_internal_energy              yes
internal_energy_rep_exp          12
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
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
simplex_max_iterations           1000
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_random_seed              0
atom_model                       all
vdw_defn_file                    vdw_AMBER_parm99.defn
flex_defn_file                   flex.defn
flex_drive_file                  flex_drive.tbl
ligand_outfile_prefix            rigid.dock2grid
write_orientations               no
num_scored_conformers            5000
write_conformations              no
cluster_conformations            yes
cluster_rmsd_threshold           2.0
rank_ligands                     no











ligand_atom_file                      ligand.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                    spheres.sph
max_orientations                      1000
critical_points                       no
chemical_matching                     no
use_ligand_spheres                    no
use_internal_energy                   yes
internal_energy_rep_exp               12
flexible_ligand                       yes
min_anchor_size                       5
pruning_use_clustering                yes
pruning_max_orients                   1000
pruning_clustering_cutoff             100
pruning_conformer_score_cutoff        100.0
use_clash_overlap                     no
print_growth_tree                     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
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_grow_tors_premin_iterations   0
simplex_random_seed                   0
atom_model                            all
vdw_defn_file                         vdw_AMBER_parm99.defn
flex_defn_file                        flex.defn
flex_drive_file                       flex_drive.tbl
ligand_outfile_prefix                 flex.dock2grid
write_orientations                    no
num_scored_conformers                 5000
write_conformations                   no
cluster_conformations                 yes
cluster_rmsd_threshold                2.0
rank_ligands                          no 

Minimizing on receptor coordinates

In order to remove any grid artifacts, you can minimize your ligand poses on the actual receptor coordinates. For this, set grid_score_primary=no, and select continuous_score as your primary scoring function. DOCK will ask you for a receptor mol2 file instead of a grid prefix. Do not use this for actual docking, as it will be very very slow. Instead, this is meant to rescore poses already generated by docking to the grid. You can also minimize the native ligand pose from the crystal structure to get a reference DOCK score.

Minimizing on the receptor coordinates may change your scores significantly in many cases, and when you are ranking several poses, might even change which pose is the top ranked pose.