Representative pubchem structure | Error in enumerating valence parameter | Missing SMARTS and probable solution |
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https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure  | | Code Block |
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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: [#7X2:1]=[#7X3+1:2]-[#6X4:3]-[*:4]. One solution can be to make t51: [*:1]-[#6X4:2]-[#7X3:3]-[*:4]" more general by
t51_edit: [*:1]~[#6X4:2]-[#7X3:3]~[*:4]"
(opls has itcan parameterize) |
https://pubchem.ncbi.nlm.nih.gov/compound/67166915  | | Code Block |
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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:[#8X1:1]=[#7X3+1:2]-[#15X4:3]. a18 is "[*:1]-[#7X4,#7X3,#7X2-1:2]-[*:3]" , can make it more general "[*:1]~[#7X4,#7X3,#7X2-1:2]~[*:3]" (even opls doesn’t have) |
https://pubchem.ncbi.nlm.nih.gov/compound/118984389#section=2D-Structure  | | Code Block |
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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: [#6:1]~[#7X2:2]-[#7X4+1:3]~[#6:4]. Making t138: "[*:1]~[#7X2:2]-[#7X3:3]~[*:4]" to include #7X4 as well in the third position, "[*:1]~[#7X2:2]-[#7X3,#7X4:3]~[*:4]", can be a general solution, but that would be mixing multiplicities, so a new parameter can be t138a: "[*:1]~[#7X2:2]-[#7X4:3]~[*:4]" (opls has itcan parameterize) |
https://pubchem.ncbi.nlm.nih.gov/compound/104806#section=2D-Structure  | | Code Block |
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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: "[#8X2:1]-[#8X1-1:2]". The bond parameter b43: "[#8X2:1]-[#8X2:2]" can be made more general by making it "[#8X2:1]-[#8X2,#8X1-1:2]" (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  | | Code Block |
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UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms:
- Topology indices (3, 6): names and elements ( N), ( S),
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| Specific smarts pattern is [#16X1-1:1]-[#7X3:2]. Can be resolved by modifying b53: "[#16X2:1]-[#7:2]" to a more general "[#16X2,#16X1-1:1]-[#7:2]". (even opls doesn’t have) |
https://pubchem.ncbi.nlm.nih.gov/compound/135436526#section=IUPAC-Name  | | Code Block |
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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 "[*:1]-[#7X3:2]-[#7X3+1:3]-[*:4]". Can be resolved by making t130 : "[*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4]" more general by making the single bonds flexible, "[*:1]~[#7X4,#7X3:2]-[#7X4,#7X3:3]~[*:4]". (opls can parameterize) |