I've been running autodock to see how certain sugars, such as malate, and citrate bind to a protein of interest. Everything is goes great until the actual step where I run autodock, and it returns the error "The two atoms defining torsion 2 are the same". I'm not exactly sure what is going on, or how to fix it. It seems to be an issue of these ligands, because if I run the exact same code with other ligands, it works fine (granted the other ligands don't bind ideally to the protein, as they're not supposed to).

Is it because these ligands I'm testing are symmetrical so as it's the different torsions, it comes across an identical torsion and then returns that error