3.1.5.1 Linkage Atom Naming

It is important to understand how to make references to adjacent residues when constructing a topology file. The following table lists the possible prefixes which may used. Note that the actual atoms referenced are not determined until the generation of segments, see Generate Command.

+

The next residue in the sequence.

-

The previous residue in the sequence.

#

Two residues forward in the sequence.

=

Two residues backward in the sequence.

+n

n residues forward in the sequence. Note that `+' sign is mandatory.

-n

n residue backward in the sequence.

No reference will be made beyond the end of a segment. In the case of cyclic peptide, CONGEN will wrap around the sequence in the appropriate direction.