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.
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Representative pubchem structure
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Error in enumerating valence parameter
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Missing SMARTS and probable solution
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https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure
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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), |
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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]"
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https://pubchem.ncbi.nlm.nih.gov/compound/67166915
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Forcefield with the following modifications:
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<!-- modification: b43 changed from [#8X2:1]-[#8X2:2] to [#8X2:1]-[#8X2,#8X1-1:2] -->
<!-- modification: b53 changed from [#16X2:1]-[#7:2] to [#16X2,#16X1-1:1]-[#7:2] -->
<!-- modification: a18 changed from [*:1]-[#7X4,#7X3,#7X2-1:2]-[*:3] to [*:1]~[#7X4,#7X3,#7X2-1:2]~[*:3] -->
<!-- modification: t51 changed from [*:1]-[#6X4:2]-[#7X3:3]-[*:4] to [*:1]~[#6X4:2]-[#7X3:3]~[*:4] -->
<!-- modification: t130 changed from [*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4] to [*:1]~[#7X4,#7X3:2]-[#7X4,#7X3:3]~[*:4] -->
<!-- modification: t138a as a child parameter to include [#7X2]-[#7X4] chemistry, other general force fields can parameterize this -->
<!-- modification: new parameters for bridgehead Nitrogen chemistry based on t134 and t138 and tweaking the central Nitrogen to be 7x3 -->
<!-- modification: t161 changed from "[*:1]~[#7X3:2]-[#15:3]~[*:4]" to "[*:1]~[#7:2]-[#15:3]~[*:4]" to make it more general --> |
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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  |
| Specific smarts: a17 is | https://pubchem.ncbi.nlm.nih.gov/compound/118984389#section=2D-Structure  |
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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.
https://pubchem.ncbi.nlm.nih.gov/compound/104806#section=2D-Structure
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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]"
Only a simple molecule 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
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UnassignedBondParameterException: BondHandler - 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
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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
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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
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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
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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
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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
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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)
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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), |
Unusual chemistry.
Found on CheMBL30 (CHEMBL331810)
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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), |
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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
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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), |
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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. t161 can be made more general.
Representative substructure of a larger molecule (along with a salt) found on CheMBL30
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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
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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 (34, 2, 1, 69): names and elements ( NC), ( P), ( C), ( SH), |
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]".
https://pubchem.ncbi.nlm.nih.gov/compound/135436526#section=IUPAC-Name
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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 (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 (25, 42, 51, 69): names and elements ( C), ( NP), ( NC), ( OH), - Topology indices (60, 51, 42, 145): names and elements ( OC), ( NC), ( NP), ( HC), |
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]".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), |
Unusual chemistry