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).