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Merge pull request #31 from molssi-seamm/dev
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Implementing atom typing for OPLSAA that were overlooked
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@seamm
seamm authored Sep 8, 2023
2 parents 4b5d5f4 + f93d95c commit fd3bb18
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13 changes: 13 additions & 0 deletions HISTORY.rst
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History
=======

2023.9.8 -- Added more typing for OPLS-AA
* cyclopropane -CH2-, -CHR-, and -CR2-
* hexafluorobenzene
* difluorobenzene
* bromobenzene
* iodobenzene
* thiophenol
* alkyl nitriles
* nitroalkanes
* nitrobenzene
* methylene in phenylacetonitrile
* corrections to methylene nitrile anion

2023.9.7 -- Added typing in OPLS_AA for fluorobenzene

2023.9.6 -- Fixed issue with PF6- geometry
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303 changes: 300 additions & 3 deletions forcefield_step/data/oplsaa.frc
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2023.01.29 1 opls_707 12.011 C 4 Nitroalkane R3C-NO2
2023.01.29 1 opls_708 14.007 N 3 Nitrobenzene -NO2
2023.01.29 1 opls_709 12.011 C 3 Nitrobenzene C-NO2
2023.01.29 1 opls_710 12.011 C 0 Benzonitrile -CH2-
2023.01.29 1 opls_710 12.011 C 0 Benzonitrile -CH2- (phenylacetonitrile?)
2023.01.29 1 opls_711 14.007 N 2 Neutral Benzamidine N
2023.01.29 1 opls_712 15.999 O 1 Propylene Carbonate C=O
2023.01.29 1 opls_713 12.011 C 3 Propylene Carbonate C=O
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"opls_363": {
"2023.01.29": {
"smarts": [
"[CD3-:1][CD2]~[ND1]"
"[CD3H2-:1][CD2]~[ND1]"
],
"description": "Nitrile anion: methyl carbon -- CH2(-)-CN",
"overrides": []
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"overrides": []
}
},
"opls_652": {
"2023.09.08": {
"smarts": [
"C1[CD4H2:1]C1"
],
"description": "cyclopropane -CH2-",
"overrides": []
}
},
"opls_653": {
"2023.09.08": {
"smarts": [
"C1[CD4H1z0:1]C1"
],
"description": "cyclopropane -CHR-",
"overrides": []
}
},
"opls_654": {
"2023.09.08": {
"smarts": [
"C1[CD4H0z0:1]C1"
],
"description": "cyclopropane -CR2-",
"overrides": []
}
},
"opls_659": {
"2023.09.07": {
"smarts": [
Expand All @@ -9246,6 +9273,249 @@
"overrides": []
}
},
"opls_661": {
"2023.09.08": {
"smarts": [
"[c:1]1(F)[c:2](F)[c:3](F)[c:4](F)[c:5](F)[c:6]1F"
],
"description": "aromatic carbon in hexafluorobenzene",
"overrides": []
}
},
"opls_662": {
"2023.09.08": {
"smarts": [
"c1([F:1])c([F:2])c([F:3])c([F:4])c([F:5])c1[F:6]"
],
"description": "fluorine in hexafluorobenzene",
"overrides": []
}
},
"opls_668": {
"2023.09.08": {
"smarts": [
"[cz0][c:1](F)[c:2](F)[cz0]"
],
"description": "aromatic carbon in difluorobenzene",
"overrides": []
}
},
"opls_669": {
"2023.09.08": {
"smarts": [
"[cz0]c([F:1])c([F:2])[cz0]"
],
"description": "fluorine in difluorobenzene",
"overrides": []
}
},
"opls_670": {
"2023.09.08": {
"smarts": [
"[c:1]Br"
],
"description": "aromatic carbon in bromobenzene",
"overrides": []
}
},
"opls_671": {
"2023.09.08": {
"smarts": [
"c[Br:1]"
],
"description": "bromine in bromobenzene",
"overrides": []
}
},
"opls_672": {
"2023.09.08": {
"smarts": [
"[c:1]I"
],
"description": "aromatic carbon in iodobenzene",
"overrides": []
}
},
"opls_673": {
"2023.09.08": {
"smarts": [
"c[I:1]"
],
"description": "iodine in iodobenzene",
"overrides": []
}
},
"opls_675": {
"2023.09.08": {
"smarts": [
"c[SH1:1]"
],
"description": "S in thiophenol",
"overrides": []
}
},
"opls_676": {
"2023.09.08": {
"smarts": [
"[c:1][SH1]"
],
"description": "aromatic carbon in thiophenol",
"overrides": []
}
},
"opls_694": {
"2023.09.08": {
"smarts": [
"[CD4][Cz1]#[N:1]"
],
"description": "N in alkyl nitrile",
"overrides": []
}
},
"opls_695": {
"2023.09.08": {
"smarts": [
"[CD4][Cz1:1]#N"
],
"description": "C in alkyl nitrile",
"overrides": []
}
},
"opls_696": {
"2023.09.08": {
"smarts": [
"[CH3:1]C#N"
],
"description": "methyl carbon in acetonitrile",
"overrides": []
}
},
"opls_697": {
"2023.09.08": {
"smarts": [
"[CD4H2z0:1]C#N"
],
"description": "methylene carbon in alkyl nitrile",
"overrides": []
}
},
"opls_698": {
"2023.09.08": {
"smarts": [
"[CD4Hz0:1]C#N"
],
"description": "methine carbon in alkyl nitrile",
"overrides": []
}
},
"opls_699": {
"2023.09.08": {
"smarts": [
"[CD4H0z0:1]C#N"
],
"description": "quaternary carbon in alkyl nitrile",
"overrides": []
}
},
"opls_700": {
"2023.09.08": {
"smarts": [
"[H:1][CD4z0]C#N"
],
"description": "hydrogen adjacent to alkyl nitrile",
"overrides": []
}
},
"opls_701": {
"2023.09.08": {
"smarts": [
"[CD4z1][ND3:1](~[OD1])~[OD1]"
],
"description": "N in nitroalkane",
"overrides": []
}
},
"opls_702": {
"2023.09.08": {
"smarts": [
"[ND3](~[OD1:1])~[OD1:2]"
],
"description": "O in nitroalkane",
"overrides": []
}
},
"opls_703": {
"2023.09.08": {
"smarts": [
"[CH3:1][ND3](~[OD1])~[OD1]"
],
"description": "C in nitromethane",
"overrides": []
}
},
"opls_704": {
"2023.09.08": {
"smarts": [
"[H:1][CD4z1][ND3](~[OD1])~[OD1]"
],
"description": "H adjacent to nitro group",
"overrides": []
}
},
"opls_705": {
"2023.09.08": {
"smarts": [
"[CD4H2:1][ND3](~[OD1])~[OD1]"
],
"description": "methylene adjacent to nitro group",
"overrides": []
}
},
"opls_706": {
"2023.09.08": {
"smarts": [
"[CD4H1:1][ND3](~[OD1])~[OD1]"
],
"description": "methine adjacent to nitro group",
"overrides": []
}
},
"opls_707": {
"2023.09.08": {
"smarts": [
"[CD4H0:1][ND3](~[OD1])~[OD1]"
],
"description": "quaternary carbon adjacent to nitro group",
"overrides": []
}
},
"opls_708": {
"2023.09.08": {
"smarts": [
"[cD3][ND3:1](~[OD1])~[OD1]"
],
"description": "N in nitrobenzene",
"overrides": []
}
},
"opls_709": {
"2023.09.08": {
"smarts": [
"[cD3:1][ND3](~[OD1])~[OD1]"
],
"description": "aromatic C in nitrobenzene",
"overrides": []
}
},
"opls_710": {
"2023.09.08": {
"smarts": [
"[cD3][CD4:1][CD2]#[ND1]"
],
"description": "C in benzonitrile -- phenylacetonitrile?",
"overrides": []
}
},
"opls_712": {
"2023.01.29": {
"smarts": [
Expand Down Expand Up @@ -9715,7 +9985,7 @@
"opls_790": {
"2023.01.29": {
"smarts": [
"[CD4H0:1]F"
"[CD4H0z1:1]F"
],
"description": "Fluorinated methine R3CF",
"overrides": []
Expand Down Expand Up @@ -9788,6 +10058,33 @@
"overrides": []
}
},
"opls_665": {
"2023.09.08": {
"smarts": [
"c1cccc[c:1]1C(F)(F)F"
],
"description": "phenyl carbon in trifluoromethylbenzene",
"overrides": []
}
},
"opls_666": {
"2023.09.08": {
"smarts": [
"c1ccccc1[C:1](F)(F)F"
],
"description": "methyl carbon in trifluoromethylbenzene",
"overrides": []
}
},
"opls_667": {
"2023.09.08": {
"smarts": [
"c1ccccc1C([F:1])([F:2])[F:3]"
],
"description": "fluorine in trifluoromethylbenzene",
"overrides": []
}
},
"opls_798": {
"2023.01.29": {
"smarts": [
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