I want to run docking in Autodock 4. What if my pdb file of protein have some new atom for which the parameter is not included? How & where can I add the parameter on my own for that atom?
A suggestion, please verify whether 'new atom' is in the proximity of ligand binding site and its in the gridbox or not. If not, you dont have to worry about it. Procedd without adding parameters and save time.