You can do it by duplicating the "first" residue after itself using mutate_insert and merge_atoms. Then mutate_replace the first residue to whatever residue it is going to be, and sam_rename to correct the residue names:
Lys2-Gly3-Glu4--- | Mut_insert (makes empty entry) Merge _atoms (duplicate coords) | v Lys2-Lys2a-Gly3-Glu4--- | Mutate_replace | v Ala2-Lys2a-Gly3-Glu4--- | Sam_rename, Move_zone (Ala1 will initially be on top of Lys2) | v Ala1-Lys2-Gly3-Glu4---
Perhaps you should do a
Write_formatted mol_* save_file ;before you start, just in case you screw up with Merge.