Certain operations within CONGEN expect the atoms in a residue to appear in a given order. Examples of such commands are the RANGE options in an atom selection, see Atom Selection, or the reading of binary coordinate files, see Read Coordinates. The ORDER command permits you to specify the atom order for all current and succeeding residues in the topology file.
Each word in the ORDER command is interpreted as a wild card atom selection token, see Atom Selection. When each residue is completed, all the atoms in the residue are matched against the words in the ORDER command. An exact match takes precedence over a wildcard match, and the last match takes precedence over earlier matches. The order of the atoms in the residue is then rearranged based on the matches into these words. If a set of atoms match the same word in the ORDER command, then these will be ordered according to their original order in the topology file.
As an example, the command
ORDER N H CA * C O
will put the amino nitrogen and hydrogen and the alpha carbon of an amino acid first, the sidechain atoms in the middle, and the carbonyl carbon and oxygen at the end of each residue.
The ORDER command takes effect starting with the next residue completed. Thus, at the beginning of a file, it affects the entire file. If specified after a RESIDUE command, it will affect that residue.