Unfortunately, it seems that the ab initio application is ignoring the ambiguous constraints. No constraints are used in the prediction and also there is not constraint score term in the final score file.
Other constraints work just fine.
Anybody encountered this before? Is there a workaround or something wrong in the way I defined the constraints?
So if you do everything identically, but just remove the AmbiguousConstraint and END_AMBIGUOUS lines from your constraint file, you see the constraints being applied, but if you add those two lines, you don’t see any of the sub-constraints being applied? I’m not sure why that would be the case – the constraint system is set up such that if subconstraints are being applied, the ambiguous constraint should also be working. Are you seeing any error messages or warnings printed?
You may need to put together a small test case which could be debugged by a developer.