Quite often, after hydrogen atoms have been added to a protein, the ionization state of various sites is not what is wanted. The ionization state of various sites in a protein can be explicitly defined by SITE=(text). The text in this case can be one or more of the entries in the table below. Entries should be separated by a comma or by a semicolon.
To neutralize all sites in a protein, use SITE=(COOH,NH2,ARG,HIS). To ionize all sites, use SITE=(COO,NH3,ARG(+),His(+)). No specific tautomer is defined - if it's not the one wanted, make the change outside MOPAC. Because atoms are added or removed, the job cannot continue. Edit the resulting <file>.out, <file>.arc, or <file>.pdb to make a new data set..
| Text | Effect | |
| COOH | Add a hydrogen atom to -COO groups | |
| COO | Remove the hydrogen atom from -COOH groups | |
| NH3 |
Add a hydrogen atom to -NH2 groups |
|
| NH2 | Remove a hydrogen atom from -NH3 groups | |
| Arg(+) | Add a hydrogen atom to -Arg- | |
| Arg | Remove a hydrogen atom from -Arg(+)- | |
| His(+) | Add a hydrogen atom to -His- | |
| His | Remove a hydrogen atom from -His(+)- |