DOCK 3.6 User Manual
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History and Changes
Here is the DOCK 3.5 manual from 1994: DOCK 3.5 Manual
Compilation
DOCK Tools
Programs, Files, and Protocols
To run DOCK 3.6 for small molcule docking and virtual screening, you need the following:
- Receptor grid (generated with delphi)
- Spheres (coloured with )
- database file containing conformational expantion of your small molecules.
DOCK 3 INPUT FILE and Parameters
Here is an example input file:
DOCK 3.5 parameter ################################################.1.A# ######### DOCK 3.6 INPUT PARAMETER FILE ############# ##############################################INPUT## # receptor_sphere_file ../../sph/match2.sph cluster_numbers 1 ligand_atom_file split_database_index output_file_prefix test. random_seed 777 # ##############################MATCHING############### # distance_tolerance 1.2 nodes_maximum 4 nodes_minimum 3 ligand_binsize 0.3 ligand_overlap 0.1 receptor_binsize 0.3 receptor_overlap 0.1 bump_maximum 1 focus_cycles 0 focus_bump 0 focus_type energy critical_clusters no # ##############################COLORING############### # chemical_matching yes case_sensitive no # ligand color, receptor color match positive negative match positive negative_or_acceptor match positive not_neutral match negative positive match negative positive_or_donor match negative not_neutral match donor acceptor match donor donacc match donor negative_or_acceptor match donor neutral_or_acceptor_or_donor match donor not_neutral match acceptor donor match acceptor donacc match acceptor positive_or_donor match acceptor neutral_or_acceptor_or_donor match acceptor not_neutral match neutral neutral match neutral neutral_or_acceptor_or_donor match ester_o donor match ester_o donacc match ester_o positive_or_donor match ester_o not_neutral match amide_o donor match amide_o donacc match amide_o positive_or_donor match amide_o not_neutral # ##############################SEARCH MODE############### # ligand_desolvation volume ratio_minimum 0.0 atom_minimum 5 atom_maximum 60 number_save 500 molecules_maximum 300000 restart_interval 10000 initial_skip 0 timeout 20 # ##############################SCORING################### # solvmap_file ../../grids/solvmap_sev delphi_file ../../grids/rec+sph2.qnifft.phi chemgrid_file_prefix ../../grids/chem vdw_parameter_file ../../grids/vdw.parms.amb.mindock check_clashes yes remove_positive_solvation no vdw_maximum 1.0e10 electrostatic_scale 1.0 vdw_scale 1.0 # ##############################MINIMIZATION############## # minimize yes minimization_max 1.0e15 check_degeneracy no simplex_iterations 1000 simplex_convergence 0.1 simplex_restart 1.0 simplex_initial_translation 0.2 simplex_initial_rotation 5.0
Parameters
Parameter Name | Discription |
---|---|
receptor_sphere_file | Sphere file. |
cluster_numbers | ?? |
ligand_atom_file | the text file that contains list of 'db.gz' files. Eg. split_database_index |
output_file_prefix | Output file prefix for the test. |
random_seed | The Simplex Minimizer requiers a random seed integer. eg.777 |
SEARCH MODE
Parameter Name | Discription |
---|---|
ligand_desolvation | volume |
ratio_minimum | 0.0 |
atom_minimum | 5 |
atom_maximum | 60 |
number_save | 500 (Maxium is 5000) |
molecules_maximum | 300000 |
restart_interval | 10000 |
initial_skip | 0 |
timeout | 20 |