If the minimizer exits with “line search abandoned" and very large van der Waals energies (in the thousands of kcal mole ), the structure probably has bad contacts. The output of X-PLOR provides a list of bad contacts . One should check the molecule and symmetry-related molecules on the graphics and fix the problem. If this is inconvenient, try the following procedure: use the “repel" nonbonded energy function (see Section 4.1) for the first several steps of minimization. One should replace the minimization statement in the example above with the following statements:
parameter nbonds repel=0.89 rcon=4. end end {*This turns on the repulsive *} {*function. *} minimize powell nstep=40 drop=40.0 end {* This switches back to the Lennard-Jones function.*} parameter nbonds repel=0.0 end end minimize powell nstep=40 drop=40.0 end
Xplor-NIH 2023-11-10