Note

This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.

PDB=(text)

Although MOZYME will normally recognize all the elements in a PDB file, the possibility exists that an element or entity will be defined in a PDB file in an unusual way, and as a result it will not be recognized. To allow for this, the keyword PDB(text) is provided. The text is composed of a series of entries of form ‘Chemical-symbol:Atomic number’, separated by commas. Thus if a PDB had some hydrogen atoms represented by the symbol J, and a bromine atom represented by QW, then these symbols would be correctly recognized by MOZYME if PDB(J:1,QW:35) were specified on the keyword line. Entities which do not correspond to elements can be excluded by assigning them the atomic number zero, e.g. PDB(LP:0) would exclude any explicitly defined lone-pairs.