Docking in 3 steps

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

Step 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.

Step 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

Step 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