To run Vina it needs to know the center of the protein and also its extents (size in XYZ directions). We can easily do this with PyMOL.
pymol -cq ./makeVinaCommandFromProtein.py proteinFile ligandFile
For high-throughput screening, where we compare each ligand to each protein, I typically wrap the script in a for-loop like:
# foreach protein in my proteins directory
for protein in proteinsDir/*; do
# foreach ligand in my ligands directory
for ligand in ligandsDir/*; do;
# make a [[MakeVinaCommand|..→]]