Make sure duplicates bondeds are set from hackblocks

Previously the rtp file could end up containing two
entries when the N/C termini databases added interactions.
These were then quicksorted, which could make the
assignment random. We now check for duplicates and
discard the rtp entry in favor of the hackblock.

Fixes #1395.

Change-Id: I505cfbb7e6c8e8050e6e2935cc417e49a515d8d8
Fixed GROMOS assignment of PRO-NH terminus torsions

This patch also adjusts the parameters for torsions
over N-CA bonds in the termini, according to
suggestions by Justin Lemkul & Drazen Petrov.

Fixes #1022.

Change-Id: Ib00d69eeddf924b1e7e2de33475d774d7da54899