You will find in this page a short tutorial for running rDock.
It has been divided in 3 steps:

1.- System Definition
2.- Cavity generation
3.- Docking

1.- System Definition

First of all, we need to define the system.
Below these lines you have an example for a DUD system of a typical prm file (See Documentation for more information):

RBT_PARAMETER_FILE_V1.00
TITLE gart_DUD

RECEPTOR_FILE gart_rdock.mol2
RECEPTOR_FLEX 3.0

##################################################################
### CAVITY DEFINITION: REFERENCE LIGAND METHOD
##################################################################
SECTION MAPPER
    SITE_MAPPER RbtLigandSiteMapper
    REF_MOL xtal-lig.sd
    RADIUS 6.0
    SMALL_SPHERE 1.0
    MIN_VOLUME 100
    MAX_CAVITIES 1
    VOL_INCR 0.0
   GRIDSTEP 0.5
END_SECTION

#################################
#CAVITY RESTRAINT PENALTY
#################################
SECTION CAVITY
    SCORING_FUNCTION RbtCavityGridSF
    WEIGHT 1.0
END_SECTION

You will need this generated “prm” file, a receptor structure mol2 file (gart_rdock.mol2) and a ligand file in the cavity (xtal-lig.sd) for going to next stage.

NOTE:
The receptor “.mol2″ file must be preparated (protonated, charged, etc.) prior to this stage. The program chosen to do so is up to the user. As a suggestion, we usually work with MOE and/or Maestro.

2.- Cavity Generation

Once the files are ready, a simple command will generate the cavity:

rbcavity -was -d -r <PRMFILE>

With the -d flag a grid “.grd” file is generated. This file can be visualized in a molecular viewer to check the generated cavity.
For example, in pymol (after loading by: pymol <RECEPTOR>.mol2 <LIGAND>.sd <GRID>.grd), write the following command in the console:

isomesh cavity, <GRID>.grd, 0.99

3.- Docking

Once the cavity is defined and generated, a 50 runs-per-ligand rDock job can be run straightforwardly with the following command:

NOTE:
The “.prm” file, receptor, reference ligand and “.as” cavity file must be in the working directory or pointed by the environmental variable “RBT_HOME”

rbdock -i <INPUT>.sd -o <OUTPUT> -r <PRMFILE> -p dock.prm -n 50