SITE=(text)

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 set by using SITE=(text).   Two formats for text are supported, either format can be used, but they cannot be mixed, that is, only one of the formats described below can be used in a given job.

The first format allows individual residues to be ionized or de-ionized. In this format, text has the form "Annn(q1[q2])[,Bmmm(q3[q4])]..." where "A" is the chain letter, "nnn" is the residue number, and "q1" and "q2" are the charges, either +, 0, or -.  If residue 123 in chain B is an Arg, then, to ionize it, use SITE=(B123(+)). If the first residue in that chain, i.e., the -NH₂ end, is also to be ionized, then use SITE=(B123(+),B1(+)). If a carboxylic acid group, e.g. an Asp at residue site D234, should also be ionized, then use SITE=(B123(+),B1(+),D234(-)). A salt bridge can be created using a construction of the form SITE=(A12(+),B34(-)). To de-ionize a site use charge "(0)" thus if the sites just described were ionized, they could then be de-ionized by using SITE=(B123(0),B1(0),D234(0)). If a residue has two ionizable sites, such as a Lys at the start of a chain, or Asp at the end of a chain, use two charges, to indicate the ionization state of each site, e.g., SITE=(B1(++),B100(--)). 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.

The second format applies to all residues with the specified groups.  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(+)). Serine, threonine, and tyrosine cannot be modified using this format.  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.