gprot.py: Ignore empty lines in topologies
gprot.py: Use set for improper_atoms
gprot.py: Clean up for readability
gprot.py,prepReader.py: Rename calc14Params to calc14NBParams
prepReader.py: Sort indexes in the same manner as pdb2gmx

This allows to easily spot differences between topologies using diff
tools. Main difference from the previous sorting order is that now
angles and dihedrals are sorted by central atoms first.