Fix #20 by ensuring CYX appears before CYS in each section

Peace is restored. Output of running with changes.
(off-dev) jeffreywagner@JW-MBP$ python test_parameterize.py 

MainChain/CYS/CYS
HarmonicBondForce 1.7237740755081177 kJ/mol
HarmonicAngleForce 3.202056646347046 kJ/mol
PeriodicTorsionForce 46.614627838134766 kJ/mol
NonbondedForce -124.68365478515625 kJ/mol
-73.14317321777344 kJ/mol
[H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])S[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 3.2020702362060547 kJ/mol
HarmonicBondForce 1.7237741947174072 kJ/mol
NonbondedForce -124.68435668945312 kJ/mol
PeriodicTorsionForce 46.614688873291016 kJ/mol
-73.143798828125 kJ/mol
79 amber dihedrals (4 impropers) and 79 off dihedrals

MainChain/CYX/CYX
HarmonicBondForce 3.0117080211639404 kJ/mol
HarmonicAngleForce 8.231612205505371 kJ/mol
PeriodicTorsionForce 106.6832046508789 kJ/mol
NonbondedForce -313.14813232421875 kJ/mol
-195.22152709960938 kJ/mol
[H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])SSC([H])([H])[C@@]([H])(C(=O)N([H])C([H])([H])[H])N([H])C(=O)C([H])([H])[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 8.23157024383545 kJ/mol
HarmonicBondForce 3.0117082595825195 kJ/mol
NonbondedForce -313.1494140625 kJ/mol
PeriodicTorsionForce 106.68318176269531 kJ/mol
-195.2230224609375 kJ/mol
162 amber dihedrals (8 impropers) and 162 off dihedrals

CTerminal/CYS/CYS
HarmonicBondForce 1.7282301187515259 kJ/mol
HarmonicAngleForce 5.558967590332031 kJ/mol
PeriodicTorsionForce 35.123416900634766 kJ/mol
NonbondedForce -133.20343017578125 kJ/mol
-90.7928466796875 kJ/mol
[H][C@@](C(=O)[O-])(C([H])([H])S[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 5.558928489685059 kJ/mol
HarmonicBondForce 1.7282299995422363 kJ/mol
NonbondedForce -133.20458984375 kJ/mol
PeriodicTorsionForce 35.123512268066406 kJ/mol
-90.79391479492188 kJ/mol
59 amber dihedrals (3 impropers) and 59 off dihedrals

CTerminal/CYX/CYX
HarmonicBondForce 3.022153615951538 kJ/mol
HarmonicAngleForce 13.915948867797852 kJ/mol
PeriodicTorsionForce 98.44212341308594 kJ/mol
NonbondedForce -294.66009521484375 kJ/mol
-179.27972412109375 kJ/mol
[H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])SSC([H])([H])[C@@]([H])(C(=O)[O-])N([H])C(=O)C([H])([H])[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 13.915891647338867 kJ/mol
HarmonicBondForce 3.022153377532959 kJ/mol
NonbondedForce -294.662109375 kJ/mol
PeriodicTorsionForce 98.44196319580078 kJ/mol
-179.2821044921875 kJ/mol
142 amber dihedrals (7 impropers) and 142 off dihedrals

NTerminal/CYS/CYS
HarmonicBondForce 1.2452521324157715 kJ/mol
HarmonicAngleForce 5.255488395690918 kJ/mol
PeriodicTorsionForce 14.086507797241211 kJ/mol
NonbondedForce 35.4573974609375 kJ/mol
56.04466247558594 kJ/mol
[H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])S[H])[N+]([H])([H])[H]
HarmonicAngleForce 5.255524635314941 kJ/mol
HarmonicBondForce 1.245252013206482 kJ/mol
NonbondedForce 35.45661926269531 kJ/mol
PeriodicTorsionForce 14.086956024169922 kJ/mol
56.04435729980469 kJ/mol
52 amber dihedrals (2 impropers) and 52 off dihedrals

NTerminal/CYX/CYX
HarmonicBondForce 2.7038345336914062 kJ/mol
HarmonicAngleForce 9.699190139770508 kJ/mol
PeriodicTorsionForce 90.61141967773438 kJ/mol
NonbondedForce -260.06146240234375 kJ/mol
-157.0469970703125 kJ/mol
[H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])SSC([H])([H])[C@@]([H])(C(=O)N([H])C([H])([H])[H])[N+]([H])([H])[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 9.699169158935547 kJ/mol
HarmonicBondForce 2.7038345336914062 kJ/mol
NonbondedForce -260.0627746582031 kJ/mol
PeriodicTorsionForce 90.61137390136719 kJ/mol
-157.04840087890625 kJ/mol
135 amber dihedrals (6 impropers) and 135 off dihedrals
openforcefield / amber-ff-porting

Fix #20 by ensuring CYX appears before CYS in each section #21
