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Check of Data and Initial
Structure and Determination of Weights
This procedure checks the initial 








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 2024-09-13