Charged ligands and receptors about autodock-vina HOT 2 CLOSED

Hi,

Excellent questions.

Docking scores are generally not to be trusted, at least not too much.

1. Yes "O" and "O-" are often the same in Vina.
2. Yes
3. The H-bond term discriminates donors from acceptors, so yes, there is some level of resolution, although the position of the H atom is ignored. For example, hydroxyl O is both donor and acceptor, pyridine N is acceptor, pyrrole N is donor, and N-methyl pyrrole N is neither.
4. No, there is no H-bond donor P, so vina has no way to model the positive charge.

Charge-charge interactions between target and ligand don't necessarily result in higher affinity, because charged groups need to be desolvated for binding. It's almost like vina got lucky by ignoring most of the physics, as most of the physics cancels itself out.

from autodock-vina.

@diogomart Thank you for the clear response. I'll close the issue in a few days if I don't have any follow-up questions.

from autodock-vina.