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 Å (60
grid points, -p 60
, spaced 0.375 Å) 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
Å. 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 .