Enable rtp angle/dihedral entries not connected by bonds

Enable rtp angle/dihedral entries not connected by bonds

pdb2gmx has previously silently ignored any angles or
torsions not connected by bonds. This patch adds code
to mark with RTP/hackblock entries that have been
assigned in this search, and afterwards we add those
that have not yet been matched. In particular, this makes
it possible to have angles or torsions in RTP entries
even if those atoms are not connected by bonds.

Fixes #1276.

Change-Id: I61c3c3954ef8c4cd59956d88b73c6a69c1a66c65