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 14.1.1).