A good way to fix two unbonded atoms at a particular distance during the optimization is doing partial optimization using opt=z-matrix. Generate the coordinates of your molecule as Z-matrix and then as Cartesian coordinates. Copy XYZ values for both atoms then past in their corresponding positions in Z-matrix i.e. mixed coordinates. By this method you gave constant values for the positions of these atoms during the optimization. Opt=z-matrix is necessary for such input file.
--- On Tue, 6/1/10, santhanamoorthi N santhanamoorthi[#]rediffmail.com <owner-chemistry~!~ccl.net> wrote: