Most of the missing parameters were found in Gen3 torsiondrive set where molecules were prepared by joining different scaffolds, which might be too artificial and may not be relevant. So here is a list of pubchem molecules matching those failed patterns and some solutions to solve those.
Forcefield with the following modifications:
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Representative pubchem structure | Error in enumerating valence parameter | Missing SMARTS and probable solution |
|---|---|---|
https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure  | Proper torsion assignment failed for [H:7][C:1]([H:8])([H:9])[N+:2](=[N:3][C:4]([H:10])([H:11])[O:5][H:12])[O-:6] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (2, 1, 0, 6): names and elements ( N), ( N), ( C), ( H), - Topology indices (2, 1, 0, 7): names and elements ( N), ( N), ( C), ( H), - Topology indices (2, 1, 0, 8): names and elements ( N), ( N), ( C), ( H), | Specific smarts: One solution can be to make
(opls can parameterize) |
https://pubchem.ncbi.nlm.nih.gov/compound/67166915  | Angle assignment failed for [H:34][c:13]1[c:12]([c:11]([c:10]([c:15]([c:14]1[H:35])[H:36])[P:8](=[O:9])([N+:16](=[O:17])[O-:18])[O:7][C:6]([H:30])([H:31])[C:5]([H:28])([H:29])[N+:2]([C:1]([H:19])([H:20])[H:21])([C:3]([H:22])([H:23])[H:24])[C:4]([H:25])([H:26])[H:27])[H:32])[H:33] AngleHandler was not able to find parameters for the following valence terms: - Topology indices (7, 15, 16): names and elements ( P), ( N), ( O), | Specific smarts: a18 is (even opls doesn’t have) |
https://pubchem.ncbi.nlm.nih.gov/compound/118984389#section=2D-Structure  | Proper torsion assignment failed for [H:26][C:10](=[C:9](/[C:8](=[N:7]/[N+:4]([C:5]([H:20])([H:21])[H:22])([C:6]([H:23])([H:24])[H:25])[C:3]([H:18])([H:19])[C:2]([H:17])([C:1]([H:14])([H:15])[H:16])[O:13][H:31])/[O-:12])[C:11]([H:28])([H:29])[H:30])[H:27] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (4, 3, 6, 7): names and elements ( C), ( N), ( N), ( C), - Topology indices (5, 3, 6, 7): names and elements ( C), ( N), ( N), ( C), - Topology indices (2, 3, 6, 7): names and elements ( C), ( N), ( N), ( C), | Specific smarts pattern: Making (opls can parameterize) |
https://pubchem.ncbi.nlm.nih.gov/compound/104806#section=2D-Structure  | Bond assignment failed for [N:1](=[O:2])[O:3][O-:4] BondHandler was not able to find parameters for the following valence terms: - Topology indices (2, 3): names and elements ( O), ( O), | Specific smarts pattern: The bond parameter (even opls doesn’t have) |
Only a simple molecule can be found on pubchem matching the [N]-[S-1] pattern, https://pubchem.ncbi.nlm.nih.gov/compound/19977646  Example from the torsion set is below and the corresponding error is in the right column  | UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms: - Topology indices (3, 6): names and elements ( N), ( S), | Specific smarts pattern is Can be resolved by modifying (even opls doesn’t have) |
https://pubchem.ncbi.nlm.nih.gov/compound/135436526#section=IUPAC-Name  | Proper torsion assignment failed for [H:11][C:1]([H:12])([H:13])[N:2]([C:3](=[N:4][H:14])[N:5]([H:15])[N+:6](=[O:7])[O-:8])[N:9]=[O:10] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (2, 4, 5, 6): names and elements ( C), ( N), ( N), ( O), - Topology indices (6, 5, 4, 14): names and elements ( O), ( N), ( N), ( H), | Specific smarts pattern is Can be resolved by making (opls can parameterize) |
 Larger molecule with this substructure found in ChemBL30 | Proper torsion assignment failed for c1ccccc1S(F)(F)(F)(F)(F) ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (4, 5, 6, 9): names and elements ( C), ( C), ( S), ( F), - Topology indices (0, 5, 6, 11): names and elements ( C), ( C), ( S), ( F), - Topology indices (0, 5, 6, 8): names and elements ( C), ( C), ( S), ( F), - Topology indices (0, 5, 6, 7): names and elements ( C), ( C), ( S), ( F), - Topology indices (4, 5, 6, 8): names and elements ( C), ( C), ( S), ( F), - Topology indices (0, 5, 6, 10): names and elements ( C), ( C), ( S), ( F), - Topology indices (4, 5, 6, 11): names and elements ( C), ( C), ( S), ( F), - Topology indices (4, 5, 6, 7): names and elements ( C), ( C), ( S), ( F), - Topology indices (0, 5, 6, 9): names and elements ( C), ( C), ( S), ( F), - Topology indices (4, 5, 6, 10): names and elements ( C), ( C), ( S), ( F), | No general torsion term for |
 Found on CheMBL30 (CHEMBL1982357) | Proper torsion assignment failed for [CH3:1][P:2](=[S:3])([CH3:4])[P:5](=[S:6])([CH3:7])[CH3:8] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (3, 1, 4, 5): names and elements ( C), ( P), ( P), ( S), - Topology indices (0, 1, 4, 5): names and elements ( C), ( P), ( P), ( S), - Topology indices (3, 1, 4, 7): names and elements ( C), ( P), ( P), ( C), - Topology indices (0, 1, 4, 7): names and elements ( C), ( P), ( P), ( C), - Topology indices (2, 1, 4, 7): names and elements ( S), ( P), ( P), ( C), - Topology indices (2, 1, 4, 6): names and elements ( S), ( P), ( P), ( C), - Topology indices (3, 1, 4, 6): names and elements ( C), ( P), ( P), ( C), - Topology indices (0, 1, 4, 6): names and elements ( C), ( P), ( P), ( C), - Topology indices (2, 1, 4, 5): names and elements ( S), ( P), ( P), ( S), | Unusual chemistry. |
 Found on CheMBL30 (CHEMBL331810)  | Proper torsion assignment failed for [H:12][c:1]1[c:2]([c:3]([c:4]2[c:5]([c:6]1[H:15])[C:7](=[O:8])[O:9][I:10]2[O:11][H:16])[H:14])[H:13] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (4, 11, 10, 8): names and elements ( C), ( I), ( O), ( C), - Topology indices (10, 11, 12, 13): names and elements ( O), ( I), ( O), ( H), - Topology indices (5, 4, 11, 10): names and elements ( C), ( C), ( I), ( O), - Topology indices (3, 4, 11, 12): names and elements ( C), ( C), ( I), ( O), - Topology indices (3, 4, 11, 10): names and elements ( C), ( C), ( I), ( O), - Topology indices (4, 11, 12, 13): names and elements ( C), ( I), ( O), ( H), - Topology indices (5, 4, 11, 12): names and elements ( C), ( C), ( I), ( O), - Topology indices (8, 10, 11, 12): names and elements ( C), ( O), ( I), ( O), Proper torsion assignment failed for [H:14][c:3]1[c:4]([c:5]([c:6]([c:7]([c:2]1[C:1]([H:11])([H:12])[H:13])[H:17])[H:16])[I:8](=[O:9])=[O:10])[H:15] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (4, 3, 13, 14): names and elements ( C), ( C), ( I), ( O), - Topology indices (4, 3, 13, 15): names and elements ( C), ( C), ( I), ( O), - Topology indices (2, 3, 13, 14): names and elements ( C), ( C), ( I), ( O), - Topology indices (2, 3, 13, 15): names and elements ( C), ( C), ( I), ( O), | Unusual chemistry |
 In conjunction with a nitro salt at CHEMBL3391852 | Proper torsion assignment failed for [H:21][c:4]1[c:5]([c:6]([c:7]([c:8]([c:3]1[O:2][C:1]([H:18])([H:19])[H:20])[H:24])[H:23])[I+:9][c:10]2[c:11]([c:12]([c:13]([c:14]([c:15]2[H:28])[H:27])[O:16][C:17]([H:29])([H:30])[H:31])[H:26])[H:25])[H:22] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (3, 14, 15, 16): names and elements ( C), ( I), ( C), ( C), - Topology indices (2, 3, 14, 15): names and elements ( C), ( C), ( I), ( C), - Topology indices (4, 3, 14, 15): names and elements ( C), ( C), ( I), ( C), - Topology indices (3, 14, 15, 20): names and elements ( C), ( I), ( C), ( C), | Unusual chemistry |
 Found on CheMBL30  | Proper torsion assignment failed for [H:19][C:7]1=[N:6][P:4](=[O:5])([O:3][C:2]([C:1]1([H:15])[H:16])([H:17])[H:18])[N:8]([C:9]([H:20])([H:21])[C:10]([H:22])([H:23])[Cl:11])[C:12]([H:24])([H:25])[C:13]([H:26])([H:27])[Cl:14] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (1, 2, 3, 4): names and elements ( C), ( N), ( P), ( O), - Topology indices (1, 2, 3, 5): names and elements ( C), ( N), ( P), ( O), - Topology indices (1, 2, 3, 12): names and elements ( C), ( N), ( P), ( N), Proper torsion assignment failed for [N:1]1=[P:2]([N:3]=[P:4]([N:5]=[P:6]1([Cl:7])[Cl:8])([Cl:9])[Cl:10])([Cl:11])[Cl:12] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (1, 0, 5, 6): names and elements ( P), ( N), ( P), ( Cl), - Topology indices (5, 4, 3, 9): names and elements ( P), ( N), ( P), ( Cl), - Topology indices (0, 1, 2, 3): names and elements ( N), ( P), ( N), ( P), - Topology indices (1, 0, 5, 7): names and elements ( P), ( N), ( P), ( Cl), - Topology indices (1, 0, 5, 4): names and elements ( P), ( N), ( P), ( N), - Topology indices (2, 3, 4, 5): names and elements ( N), ( P), ( N), ( P), - Topology indices (5, 4, 3, 8): names and elements ( P), ( N), ( P), ( Cl), - Topology indices (3, 2, 1, 11): names and elements ( P), ( N), ( P), ( Cl), - Topology indices (3, 2, 1, 10): names and elements ( P), ( N), ( P), ( Cl), | Unusual chemistry, insecticides etc. |
 Representative substructure of a larger molecule (along with a salt) found on CheMBL30 | Proper torsion assignment failed for [CH3:25][C@@H:16]1[C@H:18]([CH2:9][CH2:11][CH2:13][O:15]1)[O:20][SH+:21]([OH:22])([OH:23])[O-:24] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (23, 10, 12, 25): names and elements ( H), ( S), ( O), ( H), - Topology indices (3, 9, 10, 11): names and elements ( C), ( O), ( S), ( O), - Topology indices (11, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), - Topology indices (9, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), - Topology indices (3, 9, 10, 23): names and elements ( C), ( O), ( S), ( H), - Topology indices (13, 10, 11, 24): names and elements ( O), ( S), ( O), ( H), - Topology indices (3, 9, 10, 13): names and elements ( C), ( O), ( S), ( O), - Topology indices (23, 10, 11, 24): names and elements ( H), ( S), ( O), ( H), - Topology indices (9, 10, 11, 24): names and elements ( O), ( S), ( O), ( H), - Topology indices (13, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), - Topology indices (3, 9, 10, 12): names and elements ( C), ( O), ( S), ( O), - Topology indices (12, 10, 11, 24): names and elements ( O), ( S), ( O), ( H), | There are some occurrences of [S+] in conjunction with salts. Otherwise unusual chemistry. |
 Representative substructure of a larger molecule found on CheMBL30 | Proper torsion assignment failed for CC=[P](C)(C)(C) ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (4, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), - Topology indices (3, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), - Topology indices (0, 1, 2, 4): names and elements ( C), ( C), ( P), ( C), - Topology indices (0, 1, 2, 3): names and elements ( C), ( C), ( P), ( C), - Topology indices (5, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), - Topology indices (0, 1, 2, 5): names and elements ( C), ( C), ( P), ( C), | Unusual chemistry |
 | Proper torsion assignment failed for [CH:8](=[C:9]([O-:12])[O+:10]=[NH:11])[NH2:7] ProperTorsionHandler was not able to find parameters for the following valence terms: - Topology indices (1, 3, 4, 7): names and elements ( C), ( O), ( N), ( H), | Unusual chemistry |