How to change the residue name of a specific site?

PDB-tools
1

“pdb_rplresname” changes all residues with that name.
How can I change the residue name of a specific site?

2

Indeed all instances are changed.

You could use instead for a specific residue the pdb_mutate.py script from haddock-tools

https://github.com/haddocking/haddock-tools/blob/master/pdb_mutate.py

It will only change the residue name, but not add or remove atoms.