Pseudo atoms

In the same style as atom names, pseudo atom definitions are taken from the library file $AQUADATADIR/PseudoLIB-aqua, using the internal names of constituent atoms as a reference. Often not all pseudo atoms can be made, e.g. because a series of protons is missing from the coordinate file. Messages in aqpc.log will be:

Internal atom name not found: .....

Cannot make pseudo atom .....

resulting in the output message:

* ... pseudo atoms could not be made

* ... pseudo atoms have been made

Pseudo atoms are only generated when not all restraint atoms can be found in the coordinate file. If a pseudo atom is already present in the coordinate file, that atom will be found first, and its position will be used instead of the position calculated by Aqua.

Pseudo atom positions are calculated by averaging the coordinates of the constituent protons. The results are the same as those of the X-PLOR AVERAGE=CENTER option. No pseudo atom corrections are applied, apart from the data given in the restraint file which are interpreted in the usual SQUARE WELL manner (cf. $AQUASCRIPTSDIR/convXPLORdistrestr).