Hi Doug,
I went back to the docking step to try it again and have gotten the same result, I've attached screengrabs of what I had in my vina directory before and after doing the docking and what some of the script says. It doesn't seem to be converting the compound .sdf files to .pdbqt format and the protein_H.pdbqt file is empty as well which doesn't seem right. I've been back through all the instructions but can't see anything I've missed so I don't know where I've gone wrong.
Thanks,
Alistair
