The default list can be modified in three ways. First, interactions that are to be excluded can be placed in the topology file. This option is not recommended, because there are no check to ensure that the non-bonded exclusions for an atom are defined only above each atom. 1 or -1 include bond interactions automatically. Negative values suppress the use of the information present in the topology file.
Positive values add to the information that was in the topology file.
The residue number of a residue is its position in the list of all residues in the structure including any special termini which have been added. The linkage process involves adding bonds, bond angles, torsion angles, and non-bonded exclusions for the additional bond. Automatic Generation of Non-bonded Exclusions , for more details. An attempt has been made to ease the burden of going from residue identifiers to residue numbers which will be different for segments which have N-terminal residues added. If the two residues given are not cysteines, the residue numbers will be decremented by one, and the attempt repeated.