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.
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
|
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 |
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 |
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 |
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 |
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 |