When a small change needs to be made to a protein, for example to convert a carboxylic acid or carboxylate anion into an amide group, one way to proceed is as follows:
Start with the best geometry available, here the Starting Model should be used.
The geometry should be in PDB form, and all atoms in each residue should be contiguous. In the unlikely event that they are not, run RESEQ PDBOUT to make them contiguous.
Using an editor, e.g., notepad or vi, edit the PDB file to replace the old atom label with the new atom label. If, as is likely, the number or positions of the hydrogen atoms are now incorrect, use keyword SITE if a hydrogen atom is to be added. If a hydrogen atom needs to be deleted, delete it by editing the PDB file. Keyword SITE could be used for deleting a hydrogen atom, but it's faster to simply edit it out.
Working with the data in MOPAC format is just as easy as using PDB format, but looking at the geometries using a GUI is more difficult, so whenever possible use the PDB format.
Even small changes, such as converting a -COOH or -COO(-) into -CONH2, involve a change in empirical formula and possibly net charge. This means that comparison of heats of formation of the modified structure with that of the original structure cannot be done.
Finally, and most important: By only modifying one residue in the original geometry, no issues of ionization are involved; the original ionization states are preserved, except in the edited residue.