Enable terminus-specific atom translation

By adding protein-nterm and protein-cterm classes for atom
name translation in xlateat.dat we now avoid replacing
names such as O2 in non-standard amino acids. This patch
also corrects a cosmetic issue in the number of residues
claimed to be found in each chain by pdb2gmx.

Fixes #567.

Change-Id: I5956991e3ff3e5e1202330a857fd773f9e9b6945