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4.5.3 ADD and DELETE — Modify the Structure Arrays Syntax
     { ADD    } { BOND     }     (2A10) Fixed format
     { DELEte } { THETa    }
                { PHI      }
                { IMPHi    }
                { HBONd    }
                { DONOr    }
                { ACCEptor }
                { NONBond  }
      NCHANG   (I5)
         repeated NCHANG times Function

Most of the keywords are self explanatory. In the case on NONBOND, the nonbonded exclusions list is changed, not the actual list of nonbonded interactions. NCHANG is the number of elements to be added or deleted. NRESI specifies the residue number of the first atom, and ATOMI specifies its name. For example, deleting a peptide bond between the fourth and fifth residue would be specified as

             4 C       5 N

If a number of different internal coordinates are to be changed, separate ADD or DELE commands must be used. They can appear in any order. One must specify only as many atoms as there are in the interaction. For hydrogen bonds, only two atoms may be specified even though the proton may be explicit represented.

WARNING: This routine does not make the correct checks if you make a mistake. If you specify an atom incorrectly, or if the interaction you wish to delete is not there, the results are unpredictable. At some point, this may be fixed.