Add DOIs for OPLS atomtypes #158

summeraz · 2018-03-05T16:58:55Z

Our OPLS force field XML (which we created using atomtype definitions and parameters from GROMACS) features several atomtypes with defined SMARTS strings that lack a DOI reference. This PR adds DOIs to these atomtypes so that the source of the relevant parameters is more transparent.

summeraz · 2018-03-05T16:59:44Z

I'm not finished with this yet, but wanted to go ahead and open the PR so that I can log comments as to issues I run into trying to locate the proper DOI references.

summeraz · 2018-03-05T17:14:48Z

The sulfoxide OPLS parameters do not appear to have a published source. The GROMACS parameters that we have in our XML appear in a recent OPLS paper, where these are compared with parameters derived for the improved OPLS-AAx force field. It seems most papers in the literature that used these parameters link to this paper, where the parameters are listed in Ref. 18, although the charges used here are different than those in our XML and as listed in the 2017 paper. I went ahead and added both DOIs to this atomtype. I do not believe our XML parser is currently designed to take more than a single DOI, so I will have to update that.

Also, it might be useful to add a note attribute to Types within the AtomTypes section (unless we already have the ability to do this), so that messages (like the above) could be added if citations are not straightforward.

summeraz · 2018-03-05T17:20:16Z

Parameters for the α-carbon in alkyl pyrroles do not appear to have a published source. It appears with OPLS that for most α-carbons the epsilon and sigma used are the same as for alkane carbons and the charge is simply adjusted to preserve molecular charge neutrality. As per my above comment, this is something we could probably just add to a note attribute and link the DOI to the alkane carbon parameters.

summeraz · 2018-03-05T17:26:10Z

Parameters for cyclopropanes do not appear to have a published source. However, these parameters are identical to those for alkanes. Bonded parameters are obviously different; however, for now I'm just focusing on nonbonded parameters since we do not yet have the ability to add DOI tags to bonded parameters.

summeraz · 2018-03-05T17:54:28Z

DOIs are still needed for propylene and ethylene carbonate parameters and for alkyne parameters.

mattwthompson · 2018-03-06T03:38:14Z

And to think there was a time I thought adding SMARTS strings was the hard part!

ctk3b · 2018-03-07T22:22:53Z

Nice! Thank you for this. Now is there an easy way to review these... 🤔

justinGilmer

Phew, verified the DOI links and atom type parameters from each reference to the designated atom type here. They all look good to me.

justinGilmer · 2018-05-12T19:42:12Z

foyer/forcefields/oplsaa.xml

-  <Type name="opls_151" class="Cl" element="Cl" mass="35.453"    def="[Cl][C;X4]" desc="Cl in alkyl chlorides"  />
-  <Type name="opls_152" class="CT" element="C" mass="12.011"   def="[C;X4](Cl)([Cl,C,H])([Cl,C,H])([Cl,C,H])" desc="RCH2Cl in alkyl chlorides"  />
-  <Type name="opls_153" class="HC" element="H" mass="1.008"    def="[H][C;X4](Cl)([Cl,C,H])([Cl,C,H])" overrides="opls_140" desc="H in alkyl chlorides"  />
+  <Type name="opls_151" class="Cl" element="Cl" mass="35.453" def="[Cl][C;X4]" desc="Cl in alkyl chlorides" doi="10.1021/jp0484579"/>


justinGilmer · 2018-05-12T19:44:27Z

foyer/forcefields/oplsaa.xml

-  <Type name="opls_152" class="CT" element="C" mass="12.011"   def="[C;X4](Cl)([Cl,C,H])([Cl,C,H])([Cl,C,H])" desc="RCH2Cl in alkyl chlorides"  />
-  <Type name="opls_153" class="HC" element="H" mass="1.008"    def="[H][C;X4](Cl)([Cl,C,H])([Cl,C,H])" overrides="opls_140" desc="H in alkyl chlorides"  />
+  <Type name="opls_151" class="Cl" element="Cl" mass="35.453" def="[Cl][C;X4]" desc="Cl in alkyl chlorides" doi="10.1021/jp0484579"/>
+  <Type name="opls_152" class="CT" element="C" mass="12.011" def="[C;X4](Cl)([Cl,C,H])([Cl,C,H])([Cl,C,H])" desc="RCH2Cl in alkyl chlorides" doi="10.1021/jp0484579"/>


justinGilmer · 2018-05-12T19:45:11Z

foyer/forcefields/oplsaa.xml

-  <Type name="opls_153" class="HC" element="H" mass="1.008"    def="[H][C;X4](Cl)([Cl,C,H])([Cl,C,H])" overrides="opls_140" desc="H in alkyl chlorides"  />
+  <Type name="opls_151" class="Cl" element="Cl" mass="35.453" def="[Cl][C;X4]" desc="Cl in alkyl chlorides" doi="10.1021/jp0484579"/>
+  <Type name="opls_152" class="CT" element="C" mass="12.011" def="[C;X4](Cl)([Cl,C,H])([Cl,C,H])([Cl,C,H])" desc="RCH2Cl in alkyl chlorides" doi="10.1021/jp0484579"/>
+  <Type name="opls_153" class="HC" element="H" mass="1.008" def="[H][C;X4](Cl)([Cl,C,H])([Cl,C,H])" overrides="opls_140" desc="H in alkyl chlorides" doi="10.1021/jp0484579"/>


justinGilmer · 2018-05-12T19:49:37Z

foyer/forcefields/oplsaa.xml

@@ -686,8 +686,8 @@
  <Type name="opls_715" class="opls_715" element="H" mass="1.008"/>
  <Type name="opls_716" class="opls_716" element="C" mass="12.011"/>
  <Type name="opls_717" class="opls_717" element="H" mass="1.008"/>
-  <Type name="opls_718" class="CA" element="C" mass="12.01100"   def="[C;X3;r6]1(F)[C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6]1" overrides="opls_145"/>
-  <Type name="opls_719" class="F" element="F" mass="18.9984"   def="F[C;%opls_718]" desc="fluorobenzene F" overrides="opls_965"/>
+  <Type name="opls_718" class="CA" element="C" mass="12.01100" def="[C;X3;r6]1(F)[C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6]1" overrides="opls_145" doi="10.1021/jp0484579"/>


justinGilmer · 2018-05-12T19:49:45Z

foyer/forcefields/oplsaa.xml

-  <Type name="opls_718" class="CA" element="C" mass="12.01100"   def="[C;X3;r6]1(F)[C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6]1" overrides="opls_145"/>
-  <Type name="opls_719" class="F" element="F" mass="18.9984"   def="F[C;%opls_718]" desc="fluorobenzene F" overrides="opls_965"/>
+  <Type name="opls_718" class="CA" element="C" mass="12.01100" def="[C;X3;r6]1(F)[C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6]1" overrides="opls_145" doi="10.1021/jp0484579"/>
+  <Type name="opls_719" class="F" element="F" mass="18.9984" def="F[C;%opls_718]" desc="fluorobenzene F" overrides="opls_965" doi="10.1021/jp0484579"/>


justinGilmer · 2018-05-14T16:17:43Z

foyer/forcefields/oplsaa.xml

  <Type name="opls_906B" class="opls_906B" element="C" mass="12.011"/>
  <Type name="opls_907" class="opls_907" element="C" mass="12.011"/>
  <Type name="opls_908" class="opls_908" element="C" mass="12.011"/>
-  <Type name="opls_909" class="H" element="H" mass="1.00800"   def="H[N;%opls_900]" desc="H(N) primary amines"/>
+  <Type name="opls_909" class="H" element="H" mass="1.00800" def="H[N;%opls_900]" desc="H(N) primary amines" doi="10.1021/ja984106u"/>


justinGilmer · 2018-05-14T16:18:28Z

foyer/forcefields/oplsaa.xml

  <Type name="opls_910" class="opls_910" element="H" mass="1.008"/>
-  <Type name="opls_911" class="HC" element="H" mass="1.00800"   def="HC[N;%opls_900]" desc="H(C) for C bonded to N in amines, diamines (aziridine H2,H3)" overrides="opls_140"/>
+  <Type name="opls_911" class="HC" element="H" mass="1.00800" def="HC[N;%opls_900]" desc="H(C) for C bonded to N in amines, diamines (aziridine H2,H3)" overrides="opls_140" doi="10.1021/ja984106u"/>


justinGilmer · 2018-05-14T16:20:33Z

foyer/forcefields/oplsaa.xml

@@ -801,11 +801,11 @@
  <Type name="opls_958" class="opls_958" element="H" mass="1.008"/>
  <Type name="opls_959" class="opls_959" element="C" mass="12.011"/>
  <Type name="opls_960" class="opls_960" element="C" mass="12.011"/>
-  <Type name="opls_961" class="CT" element="C" mass="12.01100"  def="[C;X4](F)(F)(F)*" desc="perfluoroalkane CF3" overrides="opls_962"/>
-  <Type name="opls_962" class="CT" element="C" mass="12.01100"  def="[C;X4](F)(F)(*)*" desc="perfluoroalkane CF2"/>
+  <Type name="opls_961" class="CT" element="C" mass="12.01100" def="[C;X4](F)(F)(F)*" desc="perfluoroalkane CF3" overrides="opls_962" doi="10.1021/jp004071w"/>


justinGilmer · 2018-05-14T16:20:39Z

foyer/forcefields/oplsaa.xml

-  <Type name="opls_961" class="CT" element="C" mass="12.01100"  def="[C;X4](F)(F)(F)*" desc="perfluoroalkane CF3" overrides="opls_962"/>
-  <Type name="opls_962" class="CT" element="C" mass="12.01100"  def="[C;X4](F)(F)(*)*" desc="perfluoroalkane CF2"/>
+  <Type name="opls_961" class="CT" element="C" mass="12.01100" def="[C;X4](F)(F)(F)*" desc="perfluoroalkane CF3" overrides="opls_962" doi="10.1021/jp004071w"/>
+  <Type name="opls_962" class="CT" element="C" mass="12.01100" def="[C;X4](F)(F)(*)*" desc="perfluoroalkane CF2" doi="10.1021/jp004071w"/>


justinGilmer · 2018-05-14T16:21:20Z

foyer/forcefields/oplsaa.xml

  <Type name="opls_963" class="opls_963" element="C" mass="12.011"/>
  <Type name="opls_964" class="opls_964" element="C" mass="12.011"/>
-  <Type name="opls_965" class="F" element="F" mass="18.9984"  def="FC" desc="perfluoroalkane F"/>
+  <Type name="opls_965" class="F" element="F" mass="18.9984" def="FC" desc="perfluoroalkane F" doi="10.1021/jp004071w"/>


summeraz added 5 commits March 5, 2018 10:05

Added DOIs for alkyl chloride atomtypes

8b01116

Added DOIs for acetals

a4a497c

Added DOIs for sulfoxide atomtypes

b5dbe01

Added DOI for pyridine and pyrimidine atomtypes

c4383bd

Added DOI for pyrrole atomtypes

50d3acf

summeraz added 4 commits March 5, 2018 11:28

Added DOI for fluorobenzene

3018033

Added DOI for nitro and nitrile atomtypes

b586bf1

Added DOI for amine atomtypes

878e6fe

Added DOI for perfluoroalkanes

304db7a

justinGilmer approved these changes May 14, 2018

View reviewed changes

summeraz mentioned this pull request May 30, 2018

Multiple DOIs per atomtype #168

Merged

summeraz added 2 commits May 30, 2018 15:06

Add comments concerning the DOIs for certain atom types

48e563b

Merge master

4e075c3

summeraz added this to the 0.5 milestone May 30, 2018

summeraz merged commit dfc1288 into mosdef-hub:master Aug 17, 2018

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Add DOIs for OPLS atomtypes #158

Add DOIs for OPLS atomtypes #158

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Add DOIs for OPLS atomtypes #158

Add DOIs for OPLS atomtypes #158

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