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Add Smarts strings for creation of secondary and tertiary alcohols (#320
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* Add Smarts Strings to create secondary and tertiary alcohols

* Added Isopropanol and t-Butanol to implemented_opls_tests.txt

* Add top and gro files for isopropanol and t-butanol to implement tests

* Corrected name of t-butanol in test file and implemented_opls_test.txt file

* Delete blank line from foyer/tests/implemented_opls_tests.txt

Co-authored-by: Justin Gilmer <justin.b.gilmer@vanderbilt.edu>
Co-authored-by: Matt Thompson <matt.thompson@vanderbilt.edu>
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@Argon1999 @justinGilmer @mattwthompson
3 people authored Mar 12, 2020
1 parent a2ec169 commit 72c0f07
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Showing 8 changed files with 536 additions and 3 deletions.
6 changes: 3 additions & 3 deletions foyer/forcefields/xml/oplsaa.xml
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<Type name="opls_154" class="OH" element="O" mass="15.9994" def="[O;X2]H" desc="all-atom O: mono alcohols" doi="10.1021/ja9621760"/>
<Type name="opls_155" class="HO" element="H" mass="1.00800" def="H[O;%opls_154]" desc="all-atom H(O): mono alcohols, OP(=O)2" doi="10.1021/ja9621760"/>
<Type name="opls_156" class="HC" element="H" mass="1.008" def="HC(H)(H)OH" desc="all-atom H(C): methanol" overrides="opls_140" doi="10.1021/ja9621760"/>
<Type name="opls_157" class="CT" element="C" mass="12.01100" def="[C;X4]([H])([H])([*])[O;%opls_154]" desc="all-atom C: CH3 and CH2, alcohols" overrides="opls_136" doi="10.1021/ja9621760"/>
<Type name="opls_158" class="opls_158" element="C" mass="12.011"/>
<Type name="opls_159" class="opls_159" element="C" mass="12.011"/>
<Type name="opls_157" class="CT" element="C" mass="12.01100" def="[C;X4]([H])([H])([*])[O;%opls_154]" desc="all-atom C: CH3 and CH2, alcohols" overrides="opls_136, opls_159, opls_158" doi="10.1021/ja9621760"/>
<Type name="opls_158" class="CT" element="C" mass="12.011" def="[C;X4]([H])[O;%opls_154]" desc="Carbon in 2R-C(H)-OH" overrides="opls_136, opls_159" doi="10.1021/ja9621760"/>
<Type name="opls_159" class="CT" element="C" mass="12.011" def="[C;X4][O;%opls_154]" desc="Carbon in 3R-C-OH" overrides="opls_136" doi="10.1021/ja9621760"/>
<Type name="opls_160" class="opls_160" element="C" mass="12.011"/>
<Type name="opls_161" class="opls_161" element="C" mass="12.011"/>
<Type name="opls_162" class="opls_162" element="O" mass="15.9994"/>
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15 changes: 15 additions & 0 deletions foyer/opls_validation/isopropanol/isopropanol.gro
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GROningen MAchine for Chemical Simulation
12
1isopr C 1 0.231 1.061 0.363
1isopr C 2 0.185 1.206 0.371
1isopr O 3 0.044 1.212 0.347
1isopr C 4 0.215 1.266 0.507
1isopr H 5 0.207 1.018 0.265
1isopr H 6 0.179 0.999 0.438
1isopr H 7 0.338 1.053 0.380
1isopr H 8 0.234 1.264 0.293
1isopr H 9 -0.001 1.160 0.416
1isopr H 10 0.163 1.212 0.587
1isopr H 11 0.180 1.370 0.512
1isopr H 12 0.322 1.265 0.528
2.00000 2.00000 2.00000
140 changes: 140 additions & 0 deletions foyer/opls_validation/isopropanol/isopropanol.top
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;
; File isopropanol.top was generated
; By user: arjunbansal (508)
; On host: Admins-iMac.local
; At date: Tue. February 2 10:12:24 2020
;
; This is a standalone topology file
;
; Created by:
; ParmEd: slice_ch3cn.py, VERSION 3.2.0
; Executable: slice_ch3cn.py
; Library dir: /usr/local/gromacs/share/gromacs/top
; Command line:
; slice_ch3cn.py
;

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 no 1 0.5

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
opls_135 6 12.010780 0.00000000 A 0.35 0.276144
opls_158 6 12.010780 0.00000000 A 0.35 0.276144
opls_154 8 15.999430 0.00000000 A 0.312 0.71128
opls_140 1 1.007947 0.00000000 A 0.25 0.12552
opls_155 1 1.007947 0.00000000 A 1 0


[ moleculetype ]
; Name nrexcl
isopropanol 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 isopropanol rtp isopropanol q 0.0
1 opls_135 1 isopropanol C 1 -0.18000000 12.010780 ; qtot -0.180000
2 opls_158 1 isopropanol C 2 0.20500000 12.010780 ; qtot 0.025000
3 opls_154 1 isopropanol O 3 -0.68300000 15.999430 ; qtot -0.658000
4 opls_135 1 isopropanol C 4 -0.18000000 12.010780 ; qtot -0.838000
5 opls_140 1 isopropanol H 5 0.06000000 1.007947 ; qtot -0.778000
6 opls_140 1 isopropanol H 6 0.06000000 1.007947 ; qtot -0.718000
7 opls_140 1 isopropanol H 7 0.06000000 1.007947 ; qtot -0.658000
8 opls_140 1 isopropanol H 8 0.06000000 1.007947 ; qtot -0.598000
9 opls_155 1 isopropanol H 9 0.41800000 1.007947 ; qtot -0.180000
10 opls_140 1 isopropanol H 10 0.06000000 1.007947 ; qtot -0.120000
11 opls_140 1 isopropanol H 11 0.06000000 1.007947 ; qtot -0.060000
12 opls_140 1 isopropanol H 12 0.06000000 1.007947 ; qtot 0.000000

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 5 1 0.10900 284512.000000
1 7 1 0.10900 284512.000000
1 6 1 0.10900 284512.000000
1 2 1 0.15290 224262.400000
2 8 1 0.10900 284512.000000
3 2 1 0.14100 267776.000000
3 9 1 0.09450 462750.400000
4 10 1 0.10900 284512.000000
4 12 1 0.10900 284512.000000
4 2 1 0.15290 224262.400000
4 11 1 0.10900 284512.000000

[ pairs ]
; ai aj funct c0 c1 c2 c3
3 5 1 0.281000000 0.149398683
4 5 1 0.300000000 0.093088123
3 6 1 0.281000000 0.149398683
4 6 1 0.300000000 0.093088123
3 7 1 0.281000000 0.149398683
4 7 1 0.300000000 0.093088123
5 8 1 0.250000000 0.062760000
6 8 1 0.250000000 0.062760000
7 8 1 0.250000000 0.062760000
1 9 1 0.675000000 0.000000000
4 9 1 0.675000000 0.000000000
8 9 1 0.625000000 0.000000000
1 10 1 0.300000000 0.093088123
3 10 1 0.281000000 0.149398683
8 10 1 0.250000000 0.062760000
1 11 1 0.300000000 0.093088123
3 11 1 0.281000000 0.149398683
8 11 1 0.250000000 0.062760000
1 12 1 0.300000000 0.093088123
3 12 1 0.281000000 0.149398683
8 12 1 0.250000000 0.062760000

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 109.5000000 418.400000
1 2 4 1 112.7000000 488.273000
1 2 8 1 110.7000000 313.800000
2 1 5 1 110.7000000 313.800000
2 1 6 1 110.7000000 313.800000
2 1 7 1 110.7000000 313.800000
2 3 9 1 108.5000000 460.240000
2 4 10 1 110.7000000 313.800000
2 4 11 1 110.7000000 313.800000
2 4 12 1 110.7000000 313.800000
3 2 4 1 109.5000000 418.400000
3 2 8 1 109.5000000 292.880000
4 2 8 1 110.7000000 313.800000
5 1 6 1 107.8000000 276.144000
5 1 7 1 107.8000000 276.144000
6 1 7 1 107.8000000 276.144000
10 4 11 1 107.8000000 276.144000
10 4 12 1 107.8000000 276.144000
11 4 12 1 107.8000000 276.144000

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 9 3 -0.4435000 3.8325500 0.7280100 -4.1170500 0.0000000 0.0000000
1 2 4 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
1 2 4 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
1 2 4 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
3 2 1 5 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 2 1 6 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 2 1 7 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 2 4 10 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 2 4 11 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 2 4 12 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
4 2 1 5 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
4 2 1 6 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
4 2 1 7 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
4 2 3 9 3 -0.4435000 3.8325500 0.7280100 -4.1170500 0.0000000 0.0000000
5 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
6 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
7 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
8 2 3 9 3 0.9414000 2.8242000 0.0000000 -3.7656000 0.0000000 0.0000000
8 2 4 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
8 2 4 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
8 2 4 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000

[ system ]
; Name
Generic title

[ molecules ]
; Compound #mols
isopropanol 1
18 changes: 18 additions & 0 deletions foyer/opls_validation/t-butanol/t-butanol.gro
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GROningen MAchine for Chemical Simulation
15
1tbuta C 1 0.246 1.084 0.396
1tbuta C 2 0.201 1.230 0.399
1tbuta C 3 0.321 1.324 0.404
1tbuta C 4 0.114 1.262 0.277
1tbuta O 5 0.121 1.251 0.515
1tbuta H 6 0.307 1.063 0.307
1tbuta H 7 0.160 1.016 0.396
1tbuta H 8 0.305 1.060 0.485
1tbuta H 9 0.385 1.312 0.316
1tbuta H 10 0.382 1.305 0.493
1tbuta H 11 0.289 1.428 0.410
1tbuta H 12 0.170 1.247 0.184
1tbuta H 13 0.078 1.365 0.280
1tbuta H 14 0.026 1.197 0.274
1tbuta H 15 0.176 1.231 0.593
2.00000 2.00000 2.00000
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