The list of nonbonded exclusion is generated in two steps. The exclusion list can be specified in three ways. First, interactions that are to be excluded can be placed in the topology file by listing the excluded atoms after the charge. Second, NBXM mode can be specified as a qualifier to any of the commands which change internal coordinates. Third, the default NBXM value can be specified in the parameter file.
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. Added atoms are placed in the last group of the referenced residue. Any bond, angle, etc referring to deleted atoms is itself deleted. The bond, angle, etc lists are compressed. Intended to simplify the development of patches, since only bonding terms need to be specified in PRES definitions which are followed by this command.