First working commit

Seems to output valid working configurations now.
- Pseudobond parameters in PRIME20_bonded.py have been changed to
  maintain angles CO-CH-SC and NH-CH-SC rather than maintain their ratio
  with CH-SC. This works better.
- mylammps.py function create_coords now takes an argument for the space
  between each NH called res_space, and an argument for
  prototype positions called prototype_positions, and uses these
  sensibly.
- peptide_maker.py has been significantly changed to arrive at a working
  state.