The CHARMM FF often uses a patch (PRES) for simple changes that make new molecules, such as protonating Asp, or adding 3' or 5' PO4 to a chain of one or more nucleotides. What this means is that separate residues for small changes are not needed, and simple CHARMM commands (as given above by Lennart) can be used to make the change. Surely NAMD must have a patching mechanism, if it fully supports the CHARMM FF ...