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

1. Adapt to your paths to python and autodock tools in the file vina_multiligand_screen.sh
2. Prepare your receptor with the Vina plugin in PyMol and save the receptor.pdbqt file in this directory
3. Adapt the conf.txt file to fit the center and dimensions of the grid as well as the receptor file(s)
4. Put the ligands to be docked in a SD file called ligands.sdf in this directory (2D coordinates are enough)
5. 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