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openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
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[WIP] Add backbone parameters #22

Closed j-wags closed 4 years ago

j-wags commented 4 years ago

Closes #19

This PR-in-progress adds

j-wags commented 4 years ago

Current backbone OFFXML, using all tripeptides

Summary: Only three unique bonds, ~10 unique angles and impropers, but lots of proper torsions

Collapsed OFFXML (Interestingly, it won't let me post valid XML in a HTML block, so I had to mangle this by removing `<` and `>`) (off-dev) jeffreywagner@JW-MBP$ cat test_backbone.offxml ``` ?xml version="1.0" encoding="utf-8"? SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL" Bonds version="0.3" potential="harmonic" fractional_bondorder_interpolation="linear" Bond smirks="[H][N:2]([C])[C:1](=O)[C]" length="1.335 * angstrom" k="980.0 * angstrom**-2 * mole**-1 * kilocalorie" id="A14SB-MainChain_ALA_ALA-C_N"/Bond Bond smirks="[C][N:2]([C])[C:1](=O)[C]" length="1.335 * angstrom" k="980.0 * angstrom**-2 * mole**-1 * kilocalorie" id="A14SB-MainChain_ALA_PRO-C_N"/Bond Bond smirks="[C][C:1](=O)[N:2]([C])[C]" length="1.335 * angstrom" k="980.0 * angstrom**-2 * mole**-1 * kilocalorie" id="A14SB-MainChain_PRO_PRO-C_N"/Bond /Bonds Angles version="0.3" potential="harmonic" Angle smirks="[H][C@:1]([C])([C:2](=O)[N:3]([H])[C])[N]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_ALA-CX_C_N"/Angle Angle smirks="[H][C@@:3]([N:2]([C:1](=O)[C])[H])([C])[C]" angle="121.9001 * degree" k="100.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_ALA-C_N_CX"/Angle Angle smirks="[H:3][N:2]([C])[C:1](=O)[C]" angle="120.0001 * degree" k="100.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_ALA-C_N_H"/Angle Angle smirks="[H][N:3]([C])[C:2](=[O:1])[C]" angle="122.9001 * degree" k="160.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_ALA-O_C_N"/Angle Angle smirks="[H][C:3]([H])([C])[N:2]([H])[C:1](=O)[C]" angle="121.9001 * degree" k="100.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_GLY-C_N_CX"/Angle Angle smirks="[H][C@:1]([C])([C:2](=O)[N:3]([C])[C])[N]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_PRO-CX_C_N"/Angle Angle smirks="[H][C:3]([C])([N:2]([C])[C:1](=O)[C])[H]" angle="121.9001 * degree" k="100.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_PRO-C_N_CT"/Angle Angle smirks="[H][C@@:3]([C])([N:2]([C])[C:1](=O)[C])[C]" angle="121.9001 * degree" k="100.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_PRO-C_N_CX"/Angle Angle smirks="[C][N:3]([C])[C:2](=[O:1])[C]" angle="122.9001 * degree" k="160.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_ALA_PRO-O_C_N"/Angle Angle smirks="[H][C:1]([H])([C:2](=O)[N:3]([H])[C])[N]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_GLY_ALA-CX_C_N"/Angle Angle smirks="[H][C:1]([H])([C:2](=O)[N:3]([C])[C])[N]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_GLY_PRO-CX_C_N"/Angle Angle smirks="[H][C@@:1]([C])([N])[C:2](=O)[N:3]([H])[C]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_PRO_ALA-CX_C_N"/Angle Angle smirks="[H][C@@:1]([C])([N])[C:2](=O)[N:3]([C])[C]" angle="116.6 * degree" k="140.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_PRO_PRO-CX_C_N"/Angle Angle smirks="[C][C:2](=[O:1])[N:3]([C])[C]" angle="122.9001 * degree" k="160.0 * mole**-1 * radian**-2 * kilocalorie" id="A14SB-MainChain_PRO_PRO-O_C_N"/Angle /Angles ProperTorsions version="0.3" potential="k*(1+cos(periodicity*theta-phase))" default_idivf="auto" fractional_bondorder_method="AM1-Wiberg" fractional_bondorder_interpolation="linear" Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([H])[H])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ALA-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:4]([N:3]([C:2](=O)[C@@:1]([N])([C])[H])[H])([C])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_ALA-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@:1]([C])([C:2](=O)[N:3]([H:4])[C])[N]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_ALA-CX_C_N_H" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([H])[H])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ALA-C_N_CX_CT" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@:3]([C])([C:4](=O)[N])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ALA-C_N_CX_C" k1="0.0 * mole**-1 * kilocalorie" k2="0.27 * mole**-1 * kilocalorie" k3="0.42 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H:4][C@@:3]([N:2]([C:1](=O)[C])[H])([C])[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_ALA-C_N_CX_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C@:2]([C])([C:3](=O)[N:4]([H])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_ALA-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@:2]([C])([C:3](=O)[N:4]([H])[C])[N:1]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ALA-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:4]([N:3]([C:2](=[O:1])[C])[H])([C])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_ALA-O_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:4][N:3]([C])[C:2](=[O:1])[C]" periodicity1="1" periodicity2="2" phase1="0.0 * degree" phase2="180.0 * degree" id="A14SB-MainChain-ALA_ALA-O_C_N_H" k1="2.0 * mole**-1 * kilocalorie" k2="2.5 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([H])[C])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ARG-C_N_CX_C8" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([H])[S])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_CYS-C_N_CX_2C" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@:1]([C])([C:2](=O)[N:3]([H])[C:4]([H])([H])[C])[N]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_GLY-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:3]([H])([C:4](=O)[N])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_GLY-C_N_CX_C" k1="0.0 * mole**-1 * kilocalorie" k2="0.27 * mole**-1 * kilocalorie" k3="0.42 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H:4][C:3]([H])([C])[N:2]([H])[C:1](=O)[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_GLY-C_N_CX_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:3]([H:4])([C])[N:2]([H])[C:1](=O)[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_GLY-C_N_CX_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:4]([H])([C])[N:3]([H])[C:2](=[O:1])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_GLY-O_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:4]([C@:3]([N:2]([C:1](=O)[C])[H])([C])[H])([C])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_ILE-C_N_CX_3C" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([H])[c])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PHE-C_N_CX_CT" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([H])[H])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PRO-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C:4]([C])([N:3]([C])[C:2](=O)[C@:1]([H])([C])[N])[H]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_PRO-CX_C_N_CT" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:4]([C])([N:3]([C])[C:2](=O)[C@:1]([H])([C])[N])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_PRO-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:4]1([C][C][N:2]([C:3]1([H])[H])[C:1](=O)[C])[H]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CT_CT" k1="2.0 * mole**-1 * kilocalorie" k2="2.0 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H:4][C:3]([C])([N:2]([C])[C:1](=O)[C])[H]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CT_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:3]([C])([N:2]([C])[C:1](=O)[C])[H:4]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CT_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@:3]1([C:4]([C][C][N:2]1[C:1](=O)[C])([H])[H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CX_CT" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:3]([C])([N:2]([C])[C:1](=O)[C])[C:4](=O)[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CX_C" k1="0.0 * mole**-1 * kilocalorie" k2="0.27 * mole**-1 * kilocalorie" k3="0.42 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H:4][C@@:3]([C])([N:2]([C])[C:1](=O)[C])[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_PRO-C_N_CX_H1" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C@:2]([C])([C:3](=O)[N:4]([C])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-ALA_PRO-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@:2]([C])([C:3](=O)[N:4]([C])[C])[N:1]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_PRO-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C:4]([C])([N:3]([C])[C:2](=[O:1])[C])[H]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_PRO-O_C_N_CT" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:4]([C])([N:3]([C])[C:2](=[O:1])[C])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-ALA_PRO-O_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([H])[O])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_SER-C_N_CX_2C" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C@@:4]([H])([C])[O])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_THR-C_N_CX_3C" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:3]([C])([C:4]([H])([C])[C])[N:2]([H])[C:1](=O)[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ALA_VAL-C_N_CX_3C" k1="2.0 * mole**-1 * kilocalorie" k2="1.8 * mole**-1 * kilocalorie" k3="0.8 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([H])[C])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ARG_ALA-C8_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([H])[C])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ARG_PRO-C8_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([H])[S])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-CYS_ALA-2C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([H])[S])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-CYS_PRO-2C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:4]([N:3]([C:2](=O)[C:1]([N])([H])[H])[H])([C])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-GLY_ALA-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:1]([H])([C:2](=O)[N:3]([H:4])[C])[N]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-GLY_ALA-CX_C_N_H" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C:2]([H])([C:3](=O)[N:4]([H])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-GLY_ALA-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:2]([H:1])([C:3](=O)[N:4]([H])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-GLY_ALA-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:2]([H])([C:3](=O)[N:4]([H])[C])[N:1]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-GLY_ALA-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C:4]([H])([C])[N:3]([H])[C:2](=O)[C:1]([H])([H])[N]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-GLY_GLY-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:4]([C])([N:3]([C])[C:2](=O)[C:1]([H])([H])[N])[H]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-GLY_PRO-CX_C_N_CT" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:4]([C])([N:3]([C])[C:2](=O)[C:1]([H])([H])[N])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-GLY_PRO-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C:2]([H])([C:3](=O)[N:4]([C])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-GLY_PRO-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:2]([H:1])([C:3](=O)[N:4]([C])[C])[N]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-GLY_PRO-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C:2]([H])([C:3](=O)[N:4]([C])[C])[N:1]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-GLY_PRO-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C@:2]([N])([C:3](=O)[N:4]([C])[H])[H])([C])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ILE_ALA-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C@:2]([N])([C:3](=O)[N:4]([C])[C])[H])([C])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-ILE_PRO-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([H])[c])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PHE_ALA-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([H])[c])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PHE_PRO-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:1]([C])([H])[H])([N])[C:3](=O)[N:4]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PRO_ALA-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@:1]([N])([C])[C:2](=O)[N:3]([C@@:4]([C])([C])[H])[H]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-PRO_ALA-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:1]([C])([N])[C:2](=O)[N:3]([H:4])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-PRO_ALA-CX_C_N_H" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C@@:2]([C])([N])[C:3](=O)[N:4]([H])[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-PRO_ALA-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:2]([C])([N:1]([C])[C])[C:3](=O)[N:4]([H])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PRO_ALA-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C])([N])[C:2](=O)[N:3]([H])[C:4]([H])([H])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-PRO_GLY-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:2]([C:1]([C])([H])[H])([N])[C:3](=O)[N:4]([C])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PRO_PRO-CT_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C])([N])[C:2](=O)[N:3]([C])[C:4]([C])([H])[H]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-PRO_PRO-CX_C_N_CT" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:4]([C])([N:3]([C])[C:2](=O)[C@:1]([C])([N])[H])[C]" periodicity1="2" phase1="180.0 * degree" id="A14SB-MainChain-PRO_PRO-CX_C_N_CX" k1="2.5 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H:1][C@@:2]([C])([N])[C:3](=O)[N:4]([C])[C]" periodicity1="2" phase1="0.0 * degree" id="A14SB-MainChain-PRO_PRO-H1_CX_C_N" k1="0.0 * mole**-1 * kilocalorie" idivf1="1.0"/Proper Proper smirks="[H][C@@:2]([C])([N:1]([C])[C])[C:3](=O)[N:4]([C])[C]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="180.0 * degree" phase2="180.0 * degree" phase3="180.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-PRO_PRO-N_CX_C_N" k1="0.45 * mole**-1 * kilocalorie" k2="1.58 * mole**-1 * kilocalorie" k3="0.55 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([H])[O])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-SER_ALA-2C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([H])[O])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-SER_PRO-2C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C])([C@@:2]([H])([C:3](=O)[N:4]([H])[C])[N])[O]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-THR_ALA-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:1]([C])([C@@:2]([H])([C:3](=O)[N:4]([C])[C])[N])[O]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-THR_PRO-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([H])[C])([C:1]([H])([C])[C])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-VAL_ALA-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper Proper smirks="[H][C@@:2]([C:3](=O)[N:4]([C])[C])([C:1]([H])([C])[C])[N]" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.0 * degree" phase2="0.0 * degree" phase3="0.0 * degree" phase4="0.0 * degree" id="A14SB-MainChain-VAL_PRO-3C_CX_C_N" k1="0.2 * mole**-1 * kilocalorie" k2="0.2 * mole**-1 * kilocalorie" k3="0.4 * mole**-1 * kilocalorie" k4="0.0 * mole**-1 * kilocalorie" idivf1="1.0" idivf2="1.0" idivf3="1.0" idivf4="1.0"/Proper /ProperTorsions AmberImproperTorsions version="0.3" potential="k*(1+cos(periodicity*theta-phase))" default_idivf="auto" Improper smirks="[H][C@:1]([C])([C:3](=[O:4])[N:2]([H])[C])[N]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-ALA_ALA-CX_N_C_O" idivf1="1.0"/Improper Improper smirks="[H][C@@:2]([N:3]([C:1](=O)[C])[H:4])([C])[C]" periodicity1="2" phase1="180.0 * degree" k1="1.1 * mole**-1 * kilocalorie" id="A14SB-MainChain-ALA_ALA-C_CX_N_H" idivf1="1.0"/Improper Improper smirks="[H][C:2]([H])([C])[N:3]([H:4])[C:1](=O)[C]" periodicity1="2" phase1="180.0 * degree" k1="1.1 * mole**-1 * kilocalorie" id="A14SB-MainChain-ALA_GLY-C_CX_N_H" idivf1="1.0"/Improper Improper smirks="[H][C@:1]([C])([C:3](=[O:4])[N:2]([C])[C])[N]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-ALA_PRO-CX_N_C_O" idivf1="1.0"/Improper Improper smirks="[H][C@:4]1([C][C][C:2]([N:3]1[C:1](=O)[C])([H])[H])[C]" periodicity1="2" phase1="180.0 * degree" k1="1.0 * mole**-1 * kilocalorie" id="A14SB-MainChain-ALA_PRO-C_CT_N_CX" idivf1="1.0"/Improper Improper smirks="[H][C:1]([H])([C:3](=[O:4])[N:2]([H])[C])[N]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-GLY_ALA-CX_N_C_O" idivf1="1.0"/Improper Improper smirks="[H][C:1]([H])([C:3](=[O:4])[N:2]([C])[C])[N]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-GLY_PRO-CX_N_C_O" idivf1="1.0"/Improper Improper smirks="[H][C@@:1]([C])([N])[C:3](=[O:4])[N:2]([H])[C]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-PRO_ALA-CX_N_C_O" idivf1="1.0"/Improper Improper smirks="[H][C@@:1]([C])([N])[C:3](=[O:4])[N:2]([C])[C]" periodicity1="2" phase1="180.0 * degree" k1="10.5 * mole**-1 * kilocalorie" id="A14SB-MainChain-PRO_PRO-CX_N_C_O" idivf1="1.0"/Improper /AmberImproperTorsions Electrostatics version="0.3" scale12="0.0" scale13="0.0" scale14="0.833333" scale15="1.0" cutoff="9.0 * angstrom" switch_width="0.0 * angstrom" method="PME"/Electrostatics /SMIRNOFF ```

Short challenge case (MainChain ALA/CYS/PRO/GLY) test results

(summary: All errors under 3e-3 kJ/mol)

Collapsed results ``` (off-dev) jeffreywagner@JW-MBP$ python test_parameterize_tripeptides.py MainChain/ALA_GLY/ALA_GLY HarmonicBondForce 1.9712004661560059 kJ/mol HarmonicAngleForce 3.4341368675231934 kJ/mol PeriodicTorsionForce 50.509273529052734 kJ/mol NonbondedForce -148.44229125976562 kJ/mol -92.52764892578125 kJ/mol [H][C@@](C(=O)N([H])C([H])([H])C(=O)N([H])C([H])([H])[H])(C([H])([H])[H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 3.434129238128662 kJ/mol HarmonicBondForce 1.9712005853652954 kJ/mol NonbondedForce -148.44418334960938 kJ/mol PeriodicTorsionForce 50.50927734375 kJ/mol -92.5296630859375 kJ/mol 96 amber dihedrals (6 impropers) and 96 off dihedrals MainChain/ALA_PRO/ALA_PRO HarmonicBondForce 3.030322790145874 kJ/mol HarmonicAngleForce 19.63716697692871 kJ/mol PeriodicTorsionForce 100.82797241210938 kJ/mol NonbondedForce -114.08901977539062 kJ/mol 9.406494140625 kJ/mol [H][C@]1(C(C(C(N1C(=O)[C@]([H])(C([H])([H])[H])N([H])C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])C([H])([H])[H] HarmonicAngleForce 19.63718605041504 kJ/mol HarmonicBondForce 3.030322790145874 kJ/mol NonbondedForce -114.09066772460938 kJ/mol PeriodicTorsionForce 100.83116912841797 kJ/mol 9.407958984375 kJ/mol 137 amber dihedrals (6 impropers) and 137 off dihedrals MainChain/ALA_CYS/ALA_CYS HarmonicBondForce 2.6528565883636475 kJ/mol HarmonicAngleForce 4.648526668548584 kJ/mol PeriodicTorsionForce 73.26012420654297 kJ/mol NonbondedForce -124.18963623046875 kJ/mol -43.62811279296875 kJ/mol [H][C@@](C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])S[H])(C([H])([H])[H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 4.648535251617432 kJ/mol HarmonicBondForce 2.6528568267822266 kJ/mol NonbondedForce -124.1915283203125 kJ/mol PeriodicTorsionForce 73.26021575927734 kJ/mol -43.6298828125 kJ/mol 121 amber dihedrals (6 impropers) and 121 off dihedrals MainChain/GLY_ALA/GLY_ALA HarmonicBondForce 1.9718533754348755 kJ/mol HarmonicAngleForce 3.140536308288574 kJ/mol PeriodicTorsionForce 50.505401611328125 kJ/mol NonbondedForce -148.94781494140625 kJ/mol -93.33001708984375 kJ/mol [H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])[H])N([H])C(=O)C([H])([H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 3.1405320167541504 kJ/mol HarmonicBondForce 1.971853256225586 kJ/mol NonbondedForce -148.94973754882812 kJ/mol PeriodicTorsionForce 50.505401611328125 kJ/mol -93.3319091796875 kJ/mol 96 amber dihedrals (6 impropers) and 96 off dihedrals MainChain/GLY_PRO/GLY_PRO HarmonicBondForce 2.1872689723968506 kJ/mol HarmonicAngleForce 18.30342674255371 kJ/mol PeriodicTorsionForce 87.48627471923828 kJ/mol NonbondedForce -133.579345703125 kJ/mol -25.6024169921875 kJ/mol [H][C@]1(C(C(C(N1C(=O)C([H])([H])N([H])C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])C([H])([H])[H] HarmonicAngleForce 18.303451538085938 kJ/mol HarmonicBondForce 2.1872689723968506 kJ/mol NonbondedForce -133.58111572265625 kJ/mol PeriodicTorsionForce 87.48948669433594 kJ/mol -25.600830078125 kJ/mol 124 amber dihedrals (6 impropers) and 124 off dihedrals MainChain/GLY_CYS/GLY_CYS HarmonicBondForce 2.268057346343994 kJ/mol HarmonicAngleForce 4.346430778503418 kJ/mol PeriodicTorsionForce 60.68831253051758 kJ/mol NonbondedForce -145.75494384765625 kJ/mol -78.4521484375 kJ/mol [H][C@@](C(=O)N([H])C([H])([H])[H])(C([H])([H])S[H])N([H])C(=O)C([H])([H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 4.346451759338379 kJ/mol HarmonicBondForce 2.268057346343994 kJ/mol NonbondedForce -145.75677490234375 kJ/mol PeriodicTorsionForce 60.688392639160156 kJ/mol -78.453857421875 kJ/mol 108 amber dihedrals (6 impropers) and 108 off dihedrals MainChain/PRO_ALA/PRO_ALA HarmonicBondForce 2.0634169578552246 kJ/mol HarmonicAngleForce 19.256336212158203 kJ/mol PeriodicTorsionForce 99.5045166015625 kJ/mol NonbondedForce -93.092041015625 kJ/mol 27.7322998046875 kJ/mol [H][C@]1(C(C(C(N1C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])[H] HarmonicAngleForce 19.256351470947266 kJ/mol HarmonicBondForce 2.0634169578552246 kJ/mol NonbondedForce -93.0941162109375 kJ/mol PeriodicTorsionForce 99.5076904296875 kJ/mol 27.7333984375 kJ/mol 137 amber dihedrals (6 impropers) and 137 off dihedrals MainChain/PRO_GLY/PRO_GLY HarmonicBondForce 1.680991768836975 kJ/mol HarmonicAngleForce 19.149639129638672 kJ/mol PeriodicTorsionForce 86.58646392822266 kJ/mol NonbondedForce -113.290283203125 kJ/mol -5.87322998046875 kJ/mol [H][C@]1(C(C(C(N1C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])C([H])([H])C(=O)N([H])C([H])([H])[H] HarmonicAngleForce 19.149669647216797 kJ/mol HarmonicBondForce 1.6809918880462646 kJ/mol NonbondedForce -113.2923583984375 kJ/mol PeriodicTorsionForce 86.58966064453125 kJ/mol -5.87200927734375 kJ/mol 124 amber dihedrals (6 impropers) and 124 off dihedrals MainChain/PRO_CYS/PRO_CYS HarmonicBondForce 2.290161609649658 kJ/mol HarmonicAngleForce 20.404687881469727 kJ/mol PeriodicTorsionForce 109.34440612792969 kJ/mol NonbondedForce -93.92529296875 kJ/mol 38.11395263671875 kJ/mol [H][C@]1(C(C(C(N1C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])S[H] HarmonicAngleForce 20.404727935791016 kJ/mol HarmonicBondForce 2.290161609649658 kJ/mol NonbondedForce -93.92730712890625 kJ/mol PeriodicTorsionForce 109.34760284423828 kJ/mol 38.11517333984375 kJ/mol 149 amber dihedrals (6 impropers) and 149 off dihedrals MainChain/CYS_ALA/CYS_ALA HarmonicBondForce 2.5415186882019043 kJ/mol HarmonicAngleForce 4.206936836242676 kJ/mol PeriodicTorsionForce 73.31015014648438 kJ/mol NonbondedForce -121.07504272460938 kJ/mol -41.0164794921875 kJ/mol [H][C@@](C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])[H])(C([H])([H])S[H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 4.206947326660156 kJ/mol HarmonicBondForce 2.5415186882019043 kJ/mol NonbondedForce -121.07699584960938 kJ/mol PeriodicTorsionForce 73.31017303466797 kJ/mol -41.018310546875 kJ/mol 121 amber dihedrals (6 impropers) and 121 off dihedrals MainChain/CYS_GLY/CYS_GLY HarmonicBondForce 2.148588180541992 kJ/mol HarmonicAngleForce 4.29176139831543 kJ/mol PeriodicTorsionForce 60.2547607421875 kJ/mol NonbondedForce -142.6519775390625 kJ/mol -75.9569091796875 kJ/mol [H][C@@](C(=O)N([H])C([H])([H])C(=O)N([H])C([H])([H])[H])(C([H])([H])S[H])N([H])C(=O)C([H])([H])[H] HarmonicAngleForce 4.291779518127441 kJ/mol HarmonicBondForce 2.148588180541992 kJ/mol NonbondedForce -142.65377807617188 kJ/mol PeriodicTorsionForce 60.254791259765625 kJ/mol -75.95867919921875 kJ/mol 108 amber dihedrals (6 impropers) and 108 off dihedrals MainChain/CYS_PRO/CYS_PRO HarmonicBondForce 3.329922914505005 kJ/mol HarmonicAngleForce 22.3563232421875 kJ/mol PeriodicTorsionForce 111.7861557006836 kJ/mol NonbondedForce -105.27783203125 kJ/mol 32.194580078125 kJ/mol [H][C@]1(C(C(C(N1C(=O)[C@]([H])(C([H])([H])S[H])N([H])C(=O)C([H])([H])[H])([H])[H])([H])[H])([H])[H])C(=O)N([H])C([H])([H])[H] HarmonicAngleForce 22.356382369995117 kJ/mol HarmonicBondForce 3.329922914505005 kJ/mol NonbondedForce -105.27951049804688 kJ/mol PeriodicTorsionForce 111.7891845703125 kJ/mol 32.19598388671875 kJ/mol 149 amber dihedrals (6 impropers) and 149 off dihedrals ```
j-wags commented 4 years ago

Ah, this may have been prematurely merged. But it's actually looking OK. I'll open an Issue for the remaining discrepancies.