Suppose one has learned atom-based parameters for a ligand with segment identifier LIGA from Cartesian coordinates. These atom-based parameters are reduced to type-based parameters and then written to a file:
parameters reduce sele=(segid LIGA ) mode=average end end write parameters output=newparameters.pro endFor each bonded pair of chemical types, an equilibrium geometry is obtained by averaging the atom-based parameters of all the bonds in the molecular structure that match this chemical type pair. For example, in a protein, this could imply averaging over all C-C bonds in aromatic rings, or all C-O carbonyl bonds. The same averaging is done for bond angles, dihedrals and impropers, equilibrium geometries, and energy constants. Dihedral and improper periodicities will correspond to their atom-based values. The new parameter file ``newparameters.pro" can be read by X-PLOR in subsequent runs.