I was wondering that is it possible to defined hydrogen bonding of ligands with a particular residue before submitting a job in gold (in Discovery Studio Platform)? Actually, I have one ligand (juglone) and a protein. In protein there is a residue (Leucin at position 32). I would like to dock a ligand in such a way that the two oxygen atoms in a ligand can make hydrogen bonds with the hydrogen atoms in the N terminal end of the Leucine residue. So, is it possible to define previously bonding of ligands to residue in a protein??
Thanks in Advance!