This example shows how to carry out conventional refinement using a conjugate gradient minimization. The ``check.inp" protocol should be carried out before running this protocol. The repel nonbonded energy function (Eq. 4.8) should be tried if the minimization does not converge or exits with ``line search abandoned" and van der Waals energies in the thousands of kcal mole (cf. Section 13.1.1).