Dear Axel,
I checked your suggestions and this are the results:
(1) I am supposed to use a Cray version of X-plor 3.1 provided to us
by MSI.
(2) Checking the XRFILL line reveals the correct number of special
positions.
(3) I removed the constraints fix statement and ran an energy
minimization run. During this run, the number of special positions
did not change and a repel of symmetry mates did not occur. However,
when I checked the coordinates I noticed the following:
Input coordinates:
OW WAT 102 0.000 10.481 0.000 1.00 28.09
Output coordinates:
OW WAT 102 -0.279 10.494 0.216 1.00 28.09
The water drifted away from the special position and if I do not reset
manually the coordinates, the water will not be recognized as special
in any subsequent refinement run (including B-factor refinement).
Herman Schreuder
