Use case 3: covalent ligand with rigid receptor


It is assumed that you downloaded and installed MGLTools2 and the data for this tutorial and that agfr, adfr, about and pmv2 are in your PATH environment variable.

1.   Generate the target file (i.e. affinity maps and translational points)

We want to re-dock the native covalent ligand of 3c9w. Both, the receptor (3cw9.pdbqt) and ligand (3c9w_ligandWithSideChain_random.pdbqt) have been prepared for docking (i.e. PDBQT files are available).

For covalent docking, the prepared receptor and covalent ligand need to share 3 atoms as sown below. These atoms are used to transform the ligand into place with respect to the receptor to create the covalent bond.

agfr -r 3c9w.pdbqt -b user 28.565 6.329 6.985 22.5 22.5 22.5 -c 1593 1596 -t 1591 -x A:CYS164 -o 3c9w_cov_cmdline

  1. In this example we specify the box placement and size manually to illustrate this capability. Note that this is the only -b/-boxMode option for which padding is ignored.
  2. The PDB serial numbers of the 2 receptor atoms forming the covalent bond are specified using the -c/--covalentBond option. The numbers are the serial codes appearing in the pdbqt file.
  3. The third atom defining the covalent attachment is used to compute the torsion angle of the covalent bond. It is specified using the -t/--covalentBondTorsionAtom option.
  4. The -x/--covalentResidues option allows to limit the traversal of the receptor to a list or residues. This is needed sometimes as covalent residues can create bonds with the receptor other than the covalent attachment and this is the case with the native ligand of 3cw9. When agfr identifies the sub-tree beyond the covalent bond to find which atoms to cut out of the receptor for calculating affinity maps, it would include a large part of the receptor because of the spurious bond the ligand makes with the receptor and cut out in excess of 1600 atoms. The -x option prevents this from happening.

More details about running this commands are available here.


The resulting target file 4EK3_rec_FR_10_82.trg file provides a description of a rigid receptor suitable for docking (with AutoDockFR) ligands prepared for AutoDock4 into the binding site of the known ligand. The file can be inspect using the following command:

about 3c9w_cov_cmdline.trg


2.   Dock a ligand using the generated target file

Here we re-dock a known ligand, that has been randomized (i.e. its conformation as well as it positions and orientation in the crystal structure have been randomly modified). This is a proof-of-concept docking aimed at illustrating the use of adfr and verifying that the docking procedure is able to reproduce a known result.

adfr -l 3c9w_ligandWithSideChain_random.pdbqt -t 3c9w_cov_cmdline.trg --jobName covalent -C 1 2 3 --nbRuns 8 --maxEvals 100000 -O --seed 1

Details about this calculation are available here.


  1. adfr detects and, by default, will use all the cores on the computer to perform 8 Genetic Algorithms evolutions, each using up to 200'000 evaluations of the scoring function. The default number of runs is 50 and each run can use up to 2.5 million evaluations by default. These parameters are set to lower values for the tutorial for the docking to terminate faster and to prevent all runs to converge to the same solution, thus allowing us to illustrate what happens when multiple docking poses are reported.
  2. This calculation generates the following files:


The file can be inspect using the following command:

about 3c9w_ligandWithSideChain_random_covalent.dro


3.   Viewing the docking results

Docking Results Object files (.dro) can be opened by pmv2. A group is created containing the ligand and receptor molecules. Both molecules are displayed and the inter-molecular hydrogen bonds are displayed.

pmv2 3c9w_ligandWithSideChain_random_covalent.dro