Some pairs of atoms are excluded from the nbond exclusion lists because their interactions are described by other terms in the hamiltonian. By default directly bonded atoms and the 1-3 atoms of an angle are excluded from the nonbond calculation. In addition the diagonal interactions of the six membered rings in tyrosine and phenylalanine and ring atom interactions in tryptophan are excluded in the current topology files. Hydrogen bonds, and dihedral 1-4 interactions are not excluded (note that other workers may differ from us on one or both of these points).
The list of nonbonded exclusions is generated in two steps. First a
preliminary list is made at generation by
GENIC using any
information that may be present in the topology file (as for example
might be diagonal interactions in rings). The second step is an
automatic compilation of all the bond and angle interactions, followed
by a sorting of the list, performed in
MAKINB. The list is
stored in the linked list pair
points to the last exclusion in
INB to atom
i. If the
list is modified after
MAKINB, then either
be called again to resort the list, or care must be taken to see that
INB list is ascending with all
INB entries having
higher atom numbers than
i and that all atoms have at least one
MAKINB is called by default after any operation which changes
internal coordinates such as generate, patch, edit, or splice.
The default list can be modified in three ways. First, interactions that are to be excluded can be placed in the topology file. Second, the NBXMOD option can be specified as a qualifier to any of the commands which change internal coordinates. Its values and actions are:
MAKINBwill correct this automatically.
Note that the 1-3 and 1-4 interactions are determined from examination of the bond list regardless of any torsions or improper torsions which are defined.
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. If NBXMOD is not specified for a command, it defaults to 2.
The third way to change exclusions is the use of the EDIT command, see Edit Command.