1/ You did the right thing, there is no other way to do it. Using the two selections is not all that difficult, is it?
2/ Use a COOR HBOND (without keyword VERBose) in a CHARMM loop and write the number of hydrogen bonds (available as a CHARMM substitution variable, see subst.doc) to a file.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden