Missing parameters in current force field

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: `[#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	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	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	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	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	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	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)	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 torsion
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),
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),
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),
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.
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),	This is weird since the double bond is perceived as rotatable bond, might be a backend issue.
	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.