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Argon1999justinGilmermattwthompson
authoredMar 12, 2020
Add Smarts strings for creation of secondary and tertiary alcohols (#320)
* 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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Diff for: ‎foyer/forcefields/xml/oplsaa.xml

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Original file line numberDiff line numberDiff line change
@@ -154,9 +154,9 @@
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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"/>
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<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"/>
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<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"/>
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<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"/>
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<Type name="opls_158" class="opls_158" element="C" mass="12.011"/>
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<Type name="opls_159" class="opls_159" element="C" mass="12.011"/>
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<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"/>
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<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"/>
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<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"/>
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<Type name="opls_160" class="opls_160" element="C" mass="12.011"/>
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<Type name="opls_161" class="opls_161" element="C" mass="12.011"/>
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<Type name="opls_162" class="opls_162" element="O" mass="15.9994"/>

Diff for: ‎foyer/opls_validation/isopropanol/isopropanol.gro

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GROningen MAchine for Chemical Simulation
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12
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1isopr C 1 0.231 1.061 0.363
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1isopr C 2 0.185 1.206 0.371
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1isopr O 3 0.044 1.212 0.347
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1isopr C 4 0.215 1.266 0.507
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1isopr H 5 0.207 1.018 0.265
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1isopr H 6 0.179 0.999 0.438
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1isopr H 7 0.338 1.053 0.380
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1isopr H 8 0.234 1.264 0.293
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1isopr H 9 -0.001 1.160 0.416
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1isopr H 10 0.163 1.212 0.587
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1isopr H 11 0.180 1.370 0.512
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1isopr H 12 0.322 1.265 0.528
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2.00000 2.00000 2.00000

Diff for: ‎foyer/opls_validation/isopropanol/isopropanol.top

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;
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; File isopropanol.top was generated
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; By user: arjunbansal (508)
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; On host: Admins-iMac.local
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; At date: Tue. February 2 10:12:24 2020
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;
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; This is a standalone topology file
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;
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; Created by:
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; ParmEd: slice_ch3cn.py, VERSION 3.2.0
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; Executable: slice_ch3cn.py
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; Library dir: /usr/local/gromacs/share/gromacs/top
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; Command line:
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; slice_ch3cn.py
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;
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[ defaults ]
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 3 no 1 0.5
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[ atomtypes ]
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; name at.num mass charge ptype sigma epsilon
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opls_135 6 12.010780 0.00000000 A 0.35 0.276144
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opls_158 6 12.010780 0.00000000 A 0.35 0.276144
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opls_154 8 15.999430 0.00000000 A 0.312 0.71128
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opls_140 1 1.007947 0.00000000 A 0.25 0.12552
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opls_155 1 1.007947 0.00000000 A 1 0
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[ moleculetype ]
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; Name nrexcl
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isopropanol 3
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[ atoms ]
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; nr type resnr residue atom cgnr charge mass typeB chargeB massB
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; residue 1 isopropanol rtp isopropanol q 0.0
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1 opls_135 1 isopropanol C 1 -0.18000000 12.010780 ; qtot -0.180000
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2 opls_158 1 isopropanol C 2 0.20500000 12.010780 ; qtot 0.025000
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3 opls_154 1 isopropanol O 3 -0.68300000 15.999430 ; qtot -0.658000
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4 opls_135 1 isopropanol C 4 -0.18000000 12.010780 ; qtot -0.838000
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5 opls_140 1 isopropanol H 5 0.06000000 1.007947 ; qtot -0.778000
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6 opls_140 1 isopropanol H 6 0.06000000 1.007947 ; qtot -0.718000
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7 opls_140 1 isopropanol H 7 0.06000000 1.007947 ; qtot -0.658000
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8 opls_140 1 isopropanol H 8 0.06000000 1.007947 ; qtot -0.598000
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9 opls_155 1 isopropanol H 9 0.41800000 1.007947 ; qtot -0.180000
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10 opls_140 1 isopropanol H 10 0.06000000 1.007947 ; qtot -0.120000
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11 opls_140 1 isopropanol H 11 0.06000000 1.007947 ; qtot -0.060000
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12 opls_140 1 isopropanol H 12 0.06000000 1.007947 ; qtot 0.000000
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[ bonds ]
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; ai aj funct c0 c1 c2 c3
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1 5 1 0.10900 284512.000000
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1 7 1 0.10900 284512.000000
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1 6 1 0.10900 284512.000000
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1 2 1 0.15290 224262.400000
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2 8 1 0.10900 284512.000000
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3 2 1 0.14100 267776.000000
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3 9 1 0.09450 462750.400000
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4 10 1 0.10900 284512.000000
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4 12 1 0.10900 284512.000000
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4 2 1 0.15290 224262.400000
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4 11 1 0.10900 284512.000000
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[ pairs ]
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; ai aj funct c0 c1 c2 c3
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3 5 1 0.281000000 0.149398683
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4 5 1 0.300000000 0.093088123
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3 6 1 0.281000000 0.149398683
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4 6 1 0.300000000 0.093088123
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3 7 1 0.281000000 0.149398683
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4 7 1 0.300000000 0.093088123
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5 8 1 0.250000000 0.062760000
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6 8 1 0.250000000 0.062760000
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7 8 1 0.250000000 0.062760000
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1 9 1 0.675000000 0.000000000
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4 9 1 0.675000000 0.000000000
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8 9 1 0.625000000 0.000000000
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1 10 1 0.300000000 0.093088123
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3 10 1 0.281000000 0.149398683
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8 10 1 0.250000000 0.062760000
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1 11 1 0.300000000 0.093088123
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3 11 1 0.281000000 0.149398683
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8 11 1 0.250000000 0.062760000
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1 12 1 0.300000000 0.093088123
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3 12 1 0.281000000 0.149398683
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8 12 1 0.250000000 0.062760000
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[ angles ]
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; ai aj ak funct c0 c1 c2 c3
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1 2 3 1 109.5000000 418.400000
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1 2 4 1 112.7000000 488.273000
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1 2 8 1 110.7000000 313.800000
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2 1 5 1 110.7000000 313.800000
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2 1 6 1 110.7000000 313.800000
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2 1 7 1 110.7000000 313.800000
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2 3 9 1 108.5000000 460.240000
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2 4 10 1 110.7000000 313.800000
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2 4 11 1 110.7000000 313.800000
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2 4 12 1 110.7000000 313.800000
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3 2 4 1 109.5000000 418.400000
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3 2 8 1 109.5000000 292.880000
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4 2 8 1 110.7000000 313.800000
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5 1 6 1 107.8000000 276.144000
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5 1 7 1 107.8000000 276.144000
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6 1 7 1 107.8000000 276.144000
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10 4 11 1 107.8000000 276.144000
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10 4 12 1 107.8000000 276.144000
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11 4 12 1 107.8000000 276.144000
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[ dihedrals ]
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; ai aj ak al funct c0 c1 c2 c3 c4 c5
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1 2 3 9 3 -0.4435000 3.8325500 0.7280100 -4.1170500 0.0000000 0.0000000
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1 2 4 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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1 2 4 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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1 2 4 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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3 2 1 5 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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3 2 1 6 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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3 2 1 7 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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3 2 4 10 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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3 2 4 11 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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3 2 4 12 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
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4 2 1 5 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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4 2 1 6 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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4 2 1 7 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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4 2 3 9 3 -0.4435000 3.8325500 0.7280100 -4.1170500 0.0000000 0.0000000
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5 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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6 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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7 1 2 8 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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8 2 3 9 3 0.9414000 2.8242000 0.0000000 -3.7656000 0.0000000 0.0000000
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8 2 4 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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8 2 4 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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8 2 4 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
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[ system ]
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; Name
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Generic title
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[ molecules ]
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; Compound #mols
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isopropanol 1

Diff for: ‎foyer/opls_validation/t-butanol/t-butanol.gro

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GROningen MAchine for Chemical Simulation
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15
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1tbuta C 1 0.246 1.084 0.396
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1tbuta C 2 0.201 1.230 0.399
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1tbuta C 3 0.321 1.324 0.404
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1tbuta C 4 0.114 1.262 0.277
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1tbuta O 5 0.121 1.251 0.515
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1tbuta H 6 0.307 1.063 0.307
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1tbuta H 7 0.160 1.016 0.396
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1tbuta H 8 0.305 1.060 0.485
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1tbuta H 9 0.385 1.312 0.316
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1tbuta H 10 0.382 1.305 0.493
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1tbuta H 11 0.289 1.428 0.410
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1tbuta H 12 0.170 1.247 0.184
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1tbuta H 13 0.078 1.365 0.280
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1tbuta H 14 0.026 1.197 0.274
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1tbuta H 15 0.176 1.231 0.593
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2.00000 2.00000 2.00000

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