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 can 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 can 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),
|
| 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) |
 Larger molecule with this substructure found in ChemBL30 | | Code Block |
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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 [#6X3]-[#16] central bond. It’s always either #16{X1-1, X2, X3, X3+1 X4] or [#6X3]=[#16]. Can be a new generic parameter before t107. |
 Found on CheMBL30 (CHEMBL1982357) | | Code Block |
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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), |
| May need a P-P central bond generic torsionUnusual chemistry. |
 Found on CheMBL30 (CHEMBL331810)  | | Code Block |
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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), |
| Code Block |
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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 | | Code Block |
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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 
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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), |
| Code Block |
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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 | | Code Block |
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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 | | Code Block |
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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), |
| This is weird since the double bond is perceived as rotatable bond, might be a backend issue. Unusual chemistry |
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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), |
| Again double bond is perceived as rotatable bond.Unusual chemistry |