Page Comparison

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

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Error in enumerating valence parameter

...

Missing SMARTS and probable solution

...

https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure

...

Code Block

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 it

...

https://pubchem.ncbi.nlm.nih.gov/compound/67166915

...

Forcefield with the following modifications:

Code Block

        <!-- 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 -->

View file

name	modifications_for_missing_parameters.offxml

Bond assignment failed for [N:1](=[O:2])[O:3][O-:4] BondHandler was not able to find parameters for the following valence terms:

118984389#section=2D-Structure

Image Added

Representative pubchem structure

Error in enumerating valence parameter

Missing SMARTS and probable solution

https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure

Image Added

Code Block

Proper torsion assignment failed for  [H:7][C:1]([H:8])([H:9])[N+:2](=[CN:13]([HC:194])([H:2010])([H:2111])([CO:35]([H:2212])([H:23])[H:24])[C:4]([H:25])([H:26])[H:27])[H:32])[H:33]
AngleHandlerO-:6]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (72, 1, 150, 166): names and elements ( PN), ( N), ( OC),

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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Code Block

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( 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

Image Added

Code Block

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 ( CP), ( N), ( NO), ( C),

Specific smarts pattern:[#6#8X1:1]~=[#7X2#7X3+1:2]-[#7X4+1#15X4:3]~[#6:4].

Making t138: a18 is "[*:1]~-[#7X4,#7X3,#7X2-1:2]-[#7X3*:3]~[*:4]" to include #7X4 as well in the third position, "" , can make it more general "[*:1]~[#7X4,#7X3,#7X2-1:2]-[#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 it

https://3]"

(even opls doesn’t have)

https://pubchem.ncbi.nlm.nih.gov/compound/104806#section=2D-Structure

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Code Block

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

Image Added

Code Block
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

Image Added

Example from the torsion set is below and the corresponding error is in the right column

Image Added

Code Block
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

Image Added

Code Block

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)

Image Added

Larger molecule with this substructure found in ChemBL30

Code Block

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.

Image Added

Found on CheMBL30 (CHEMBL1982357)

Code Block

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.

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Found on CheMBL30 (CHEMBL331810)

Image Added

Code Block

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

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

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In conjunction with a nitro salt at CHEMBL3391852

Code Block

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

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Found on CheMBL30

Image Added

Code Block

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

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.

Image Added

Representative substructure of a larger molecule (along with a salt) found on CheMBL30

Code Block

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 (212, 10, 11, 324): 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

Image Removed

Example from the torsion set is below and the corresponding error is in the right column

Image Removed

Code Block
UnassignedBondParameterException: BondHandlerS), ( O), ( H),

There are some occurrences of [S+] in conjunction with salts. Otherwise unusual chemistry.

Image Added

Representative substructure of a larger molecule found on CheMBL30

Code Block

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]".

even opls doesn’t have

https://pubchem.ncbi.nlm.nih.gov/compound/135436526#section=IUPAC-Name

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Code Block

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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Code Block

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

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