[Dock-fans] Protein-Protein Docking

[CJ Arthur]

I've been trying to dock two proteins using Dock and have hit some
problems. If possible could someone have a look at what I'm doing an tell
me what I'm doing wrong please.

Can anyone see what I'm doing wrong, or can someone send me the grid and
dock input files that they have used previously so that i can try to get
an idea of where i'm making my mistake.

Thanks in advance.

        Chris

I generate spheres around both my recetor and ligand proteins using sphgen

i then select spheres around the active site of the receptor, so that the
ligand is placed in an appropriate place

sphere_selector receptor.sph activesite.mol2 10.0

and make a pdb file of selected_spheres.sph so that i can check it in chimera
showsphere

i then use showbox with a margin of 50A, so that its big enought to hold
my ligand molecule.

I then use grid with the grid input settings listed below

And then I dock using the dock settings listed below.

What happens is that the ligand molecule is overlayed over the receptor
(its as iff the the ligand is put 'into' the spheres of the receptor.



*******
grid input

compute_grids          yes
grid_spacing           0.3
output_molecule        no
contact_score          no
energy_score           yes
energy_cutoff_distance 9999
atom_model             a
attractive_exponent    6
repulsive_exponent     12
distance_dielectric    yes
dielectric_factor      4
bump_filter            yes
bump_overlap           0.75
receptor_file          receptor.mol2
box_file               site_box.pdb
vdw_definition_file    /home/chxcja/dock6/parameters/vdw_AMBER_parm99.defn
score_grid_prefix      grid



*****
dock input

ligand_atom_file                                             ligand.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                yes
automated_matching                                           no
distance_tolerence                                           0.25
distance_minimum                                             2.0
nodes_minimum                                                3
nodes_maximum                                                10
receptor_site_file                                           activesite.sph
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           yes
ligand_sphere_file                                           ligand.sph
flexible_ligand                                              no
bump_filter                                                  yes
bump_grid_prefix                                             grid
max_bumps_anchor                                             1
max_bumps_growth                                             1
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         yes
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
dock3.5_score_primary                                        no
continuous_score_primary                                     yes
cont_score_rec_filename                                      receptor.mol2
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
cont_score_use_dist_dep_dielectric                           yes
cont_score_dielectric                                        4.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file
/home/chxcja/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file
/home/chxcja/dock6/parameters/flex.defn
flex_drive_file
/home/chxcja/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        complex_out
write_orientations                                           yes
num_primary_scored_conformers_rescored                       10
write_primary_conformations                                  yes
cluster_primary_conformations                                yes
cluster_rmsd_threshold                                       2.0
num_clusterheads_for_rescore                                 5
num_secondary_scored_conformers                              5
write_secondary_conformations                                yes
rank_primary_ligands                                         no
rank_secondary_ligands                                       no

******





--