This page was last updated on October 30th, 2019 at 11:25 pm

A simple re-docking tutorial

In this tutorial we illustrate how to re-dock a known peptide into its native receptor. We will redock a pseudophosphorylated Smad1 peptide into TPR domain of CHIP (PDB: 3Q47).

In this tutorial you will learn:

  • to generate a target file for a docking in a box defined by the known peptide.
  • to run ADCP to re-dock the peptide
  • to understand the output of an ADCP docking run


Go back to ADCP Homepage.

Convert PDB files to PDBQT files.

PDBQT file is a file format designed for AutoDock programs. Compared with standard PDB file format, PDBQT file format added two columns for the partial charge and AutoDock atom type.

In this tutorial, we will start from two separate PDB files for the receptor and the peptide. The two files are separated based on PDB file downloaded directly from PDB. Only the protein part is included in both files.

First, we will unzip the file we just downloaded.

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and go to the directory for this tutorial.

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Now, we will need to protonate both PDB files with reduce (included in the ADFRSuite).

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Then we will use two scripts prepare_ligand and prepare_receptor in ADFRSuite to convert the protonated PDB files into PDBQT files.

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Now we are ready for the next step, generating target file.

Generate the target file containing the affinity maps.

Target file is a zipped file containing everything you need for docking with ADFR and ADCP. It can be easily generated from the command line or a GUI.

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Please note this will put the docking box around the specified peptide file with a padding of 4 Angstrom. If you don’t know the peptide binding site, please checkout agfrgui tutorials.

Details: the agfr is used to position and size the docking box over the receptor pocket(s) into which we want to dock a ligand, and compute affinity maps for a given list of AutoDock4 atoms types. The maps are calculated by the AutoGrid4 program.


-r : specifies the receptor file

-l : specifies the ligand file

-asv: specifies AutoSite version number (1.0 or 1.1).   Default AutoSite version is 1.0 (if -asv option is not used)

-o : specifies the name for the target files

The receptor is specified using the –r/–receptor command line option. This option is required. The position and size of the box can be specified in a variety of ways using the –b/–boxMode option. In the example above, agfr creates the box as the bounding box of the given (known) ligand atoms (-l/–ligand). By default, a padding of 4 Å is added to every side of the bounding box. The padding value can be modified using the –P/–padding option. The padding is added on every side.

The agfr command generates a target file with a .trg extension. This file will be saved under the name specified by the –o/–output command line option. When omitted, a unique and descriptive filename will be created automatically. The target file contains the calculated affinity maps, translational points for placing the ligand in sensible places in the docking box, and meta-data about the gird size, position, spacing, receptor atoms involved, affinity maps, etc. These files can be inspected using the about command.

The translational points are computed using the AutoSite program. This program will analyze affinity maps and cluster high affinity points to identify clusters of points modeling potential binding pockets. The –p/–pocketMode allows specifying how to handle multiple clusters of affinity points representing the pockets found in the docking box. Since this option is omitted here, all clusters are merged to create a single set of translational points.

By default, maps are computed for all AutoDock4 atom types. The list of atom types for which to compute affinity maps can be set using the –m/–mapTypes option. Generating affinity maps for fewer atom types generates smaller target files and takes less time to perform the calculation. However, such a target file cannot be used for docking ligands containing atoms for which the target files does not contain the affinity map.

Running this command generates the following output (saved in 3Q47.log)

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Dock the peptide from sequence using the generated target file

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Details: adcp detects the number of cores available and by default will use them all to perform 20 independent searches (-N, —nbRuns 20) each using up to 2,500,000 evaluations of the scoring function (-n, –numSteps 2500000). By default adcp performs 50 searches, each allotted 2.5 million evaluations. Typically, more complex docking problems require more searches to be performed to increase the chances to find the best possible docked pose (i.e. global minimum of the scoring function).

This calculation generates the following files:

  • 3Q47_redocking_ranked_{num}.pdb                                # the final solutions with ranking after clustering
  • 3Q47_redocking_{num}.pdb                                               # the MC trajectory for each replica
  • 3Q47_redocking_{num}.out                                                # detailed output file for each replica


  • ADCP’s search procedure is stochastic, meaning that docking the same ligand into the same target twice can produce different results if  different random number generator seeds are used. However, the energy landscape for this receptor and ligand is the same in both runs. If both docking runs find the global minimum of this energy landscape, the solutions produced by both runs will be the same, independently of the paths taken by the search to get there. On the other hand, searches that get trapped in a local minima, yield docking poses that differ from each other. Specifying the seeds used by the random number generator (–seed) allows reproducing a docking calculation, for a given version of the code.
  • In general, we suggest running 100 replicas with 1 million steps per amino acid and starting from a mixture of extended and helical conformation.

An example output of the command is listed below:

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