Hi Boris, Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab