##

Check of Data and Initial
Structure and Determination of Weights

This procedure checks the initial value and determines the ideal
weight (and if a phase restraint is used)
between and . The procedure
should be carried out before running
any refinement on the system. The weight is determined by running a
brief molecular dynamics calculation without
and then comparing the norm of the gradient of
and the norm of the gradient of .
The program will display the weight. A similar procedure should be
applied when using targets other than the crystallographic
residual (Eq. 13.1).

check.inp

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*