Repository containing scripts for docking with Vina
- Vina for docking
- RDKit for ligand conformer generation
- Pymol with AutoDockTools / Vina plugin for receptor and ligand preparation
- Adapt to your paths to python and autodock tools in the file
vina_multiligand_screen.sh
- Prepare your receptor with the Vina plugin in PyMol and save the
receptor.pdbqt
file in this directory - Adapt the
conf.txt
file to fit the center and dimensions of the grid as well as the receptor file(s) - Put the ligands to be docked in a SD file called
ligands.sdf
in this directory (2D coordinates are enough) - run
bash vina_multiligand_screen.sh
The script will generate the following:
- A grid image of the ligands in
ligands.png
- A folder for every ligand containing the docking results
- A global
energies.txt
containing the energies for all docked conformations of the individual ligands