Why are my H-bond constraints not being taken into account?
A ligand atom may be constrained to form a hydrogen bond to a particular protein atom. One atom should be a hydrogen atom on a H-bond donor and the other should be a H-bond acceptor. The protein atom should be available for ligand binding (e.g. solvent accessible). You can see if the atoms involved in your H-bond constraint are being recognised as donors/acceptors by checking the list of proton acceptors and donors given in the gold_protein.log file. GOLD will then be biased towards finding solutions in which the specified atoms form H-bonds. However, it is important to remember that such a solution is not guaranteed.