DOCK 3.6 User Manual: Difference between revisions
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=Compilation= | ==History and Changes== | ||
[[DOCK 3.5 Changes]] | |||
[[DOCK 3.6]] | |||
Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual] {LINK NO LONGER WORKING} | |||
Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change. | |||
Using Qnifft grids with DOCK 3.5.54 may result in unresonably high electrostatic energies. So be aware of the DOCK version being used and the Electrostatic grids generation method. | |||
==Compilation== | |||
*[[Dock development]] | |||
*[[How to compile DOCK]] | |||
==DOCK Tools== | |||
[[Docking tools]] | |||
[[Flexibase Format]] | |||
= Programs, Files, and Protocols= | = Programs, Files, and Protocols= | ||
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=DOCK 3 INPUT FILE and Parameters= | =DOCK 3 INPUT FILE and Parameters= | ||
[[INDOCK for DOCK 3.6]] | |||
[[MPose]] | |||
[[Dock Ligand Clustering]] | |||
Here is an example input file: | Here is an example input file: | ||
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|- | |- | ||
|cluster_numbers | |cluster_numbers | ||
| | |This has to do with the sphere clusters. | ||
|- | |- | ||
|ligand_atom_file | |ligand_atom_file | ||
Line 127: | Line 153: | ||
|- | |- | ||
|} | |} | ||
===SEARCH MODE=== | |||
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%" | |||
|- style="background:red" | |||
! style="width 30%" !|Parameter Name | |||
! style="width:70%" !|Discription | |||
|- | |||
| mode | |||
| This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which alowed multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary [[MPose]]). The ligand clustering [[Dock Ligand Clustering]] code also alows for multiple conformations to be saved. | |||
|- | |||
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%" | |||
|- style="background:lightgreen" | |||
! style="width 30%" !|Parameter Name | |||
! style="width:70%" !|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 | |||
|- | |||
|} | |||
=DOCK 3 Scoring Function= | =DOCK 3 Scoring Function= | ||
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%" | |||
|- style="background:lightgreen" | |||
! style="width 30%" !|Parameter Name | |||
! style="width:70%" !|Discription | |||
|- | |||
| solvmap_file | |||
| solvmap_sev is . . . | |||
|- | |||
|delphi_file | |||
| rec+sph2.qnifft.phi is assumed to be gerenerated with qnifft. If delphi grids are used modify delphi_nsize | |||
|- | |||
|delphi_nsize | |||
| defult is 193. if using qnifft grids use defult. if using Delphi grids use 179. see [[Qnifft DOCK 3.6 conversion]] for more discution | |||
|- | |||
| 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 | |||
|- | |||
[[Category:DOCK]] |
Latest revision as of 22:17, 2 January 2019
History and Changes
Here is the DOCK 3.5 manual from 1994: DOCK 3.5 Manual {LINK NO LONGER WORKING}
Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see Qnifft DOCK 3.6 conversion for dicussion of this change.
Using Qnifft grids with DOCK 3.5.54 may result in unresonably high electrostatic energies. So be aware of the DOCK version being used and the Electrostatic grids generation method.
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 | This has to do with the sphere clusters. |
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 |
---|---|
mode | This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which alowed multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary MPose). The ligand clustering Dock Ligand Clustering code also alows for multiple conformations to be saved. |
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 |
DOCK 3 Scoring Function
Parameter Name | Discription |
---|---|
solvmap_file | solvmap_sev is . . . |
delphi_file | rec+sph2.qnifft.phi is assumed to be gerenerated with qnifft. If delphi grids are used modify delphi_nsize |
delphi_nsize | defult is 193. if using qnifft grids use defult. if using Delphi grids use 179. see Qnifft DOCK 3.6 conversion for more discution |
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 |