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Step 1: Docking (local)

The docking calculation between the ligand PF-07321332 ( PDB file ligand.pdb ) and the receptor 3CLpro (domain I+II) (pdb file 3clc.pdb ) is performed using Autodock4 with the wrapper bash script docking.bash:


docking.bash -l ligand -r 3clp -x -10.55 -y 20.65 -z 66.75 -p 60

The above command instructs Autodock4 to run 50 docking rounds using the Lamarckian genetic algorithm with the center of mass of the fully flexible ligand placed within a 22.5 (60 grid points, -p 60, spaced 0.375 ) side-lenght cubic box centered at the at the midpoint (-x -10.55 -y 20.65 -z 66.75) vector connecting the S(CYS145) and NE(HIS41) atoms in the receptor active site . A maximum of 2.5 million energy evaluations are applied for each docking round. Issuing the command without arguments yield the help for the script usage.


The results are clustered using the default tolerance of 2 . The lowest energy docked conformation of the lowest energy cluster is the best-docked conformation.
The script automatically generates the ligand-receptor complex pdb file with the ligand in the best (lowest binding free energy) docking pose. This is the starting input structure for the subsequent Step 2 .

N.B.: To run the docking.bash command, Autodock4 and mgltools (soft link the mgltools installdir to $HOME/mgltools ) must be installed in your computer .