Dear Xiang-Ju (and other readers),
Thanks....
I have to read the FAQ... sorry I forgot.
Solution to this problem.
If an A-T basepair is replaced by a U-U basepair in bp_helical.par, the distance between the atoms in the H-bond is too large.
The solution was to be found in FAQ#6, and is the following....
In the X3DNA/BASEPARS/misc_3dna.par
there is a line:
4.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location
I increased the upper H-bond length t0 5.0. So this line looks in my file:
5.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location
Now the basepair is detected, and the problem is solved.
Kind regards,
Ramon