Task: Add Lipid21 (openmm/openmm#5066)

org: openmm
repo: openmm
pr_number: 5066
issue_title: Add Lipid21
issue_body: Adds Lipid21 from https://github.com/openmm/openmmforcefields/pull/390.  (Presumably we shouldn't merge this PR before that one.)  In addition to adding Amber19 to the Modeller test, I've also manually checked that the updated `amber19-all.xml` can be used to add membranes of all Modeller-supported types, and to set up a stable membrane protein simulation.
resolved_issues: title: Add Lipid21
body: The Lipid21 force field is missing from the Amber19 parameter set in OpenMM, limiting the ability to simulate lipid membranes and membrane protein systems using the Amber19 force field. Users currently need to rely on AmberTools for system preparation, which adds complexity and requires external tools.

Expected behavior: The Lipid21 force field should be fully integrated into the Amber19 parameter set in OpenMM, allowing users to directly simulate lipid membranes and membrane protein systems without needing external tools for system preparation. This integration should support all membrane types compatible with the Modeller class and enable stable simulations of membrane protein systems.

## IMPORTANT INSTRUCTIONS

1. If you edit a python file, you MUST run 'make PythonInstall' inside the build directory
2. If you edit a c++ file, you MUST run 'make -j4 && make install" inside the build directory

Reference solution:
fix_patch: diff --git a/docs-source/usersguide/application/02_running_sims.rst b/docs-source/usersguide/application/02_running_sims.rst
index 1485c9f8a8..d5cbdb57ba 100644
--- a/docs-source/usersguide/application/02_running_sims.rst
+++ b/docs-source/usersguide/application/02_running_sims.rst
@@ -487,6 +487,7 @@ File                                 Parameters
 :file:`amber19/protein.ff19ipq.xml`  Protein (alternative)
 :file:`amber19/DNA.OL21.xml`         DNA\ :cite:`Zgarbova2021`
 :file:`amber14/RNA.OL3.xml`          RNA
+:file:`amber19/lipid21.xml`          Lipid
 :file:`amber14/GLYCAM_06j-1.xml`     Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007`
 :file:`amber19/tip3p.xml`            TIP3P water model\ :cite:`Jorgensen1983` and ions
 :file:`amber19/tip3pfb.xml`          TIP3P-FB water model\ :cite:`Wang2014` and ions
@@ -498,8 +499,8 @@ File                                 Parameters
 ===================================  ===========================================
 
 As a convenience, the file :file:`amber19-all.xml` can be used as a shortcut to
-include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`, and
-:file:`amber14/RNA.OL3.xml`.  In most cases, you can simply include that file,
+include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`,
+:file:`amber14/RNA.OL3.xml`, and :file:`amber19/lipid21.xml`.  In most cases, you can simply include that file,
 plus one of the water models, such as :file:`amber19/tip3pfb.xml` for the
 TIP3P-FB water model and ions\ :cite:`Wang2014`:
 ::
@@ -530,15 +531,6 @@ to them.
          you run the risk of having :class:`ForceField` throw an exception since
          :file:`tip3p.xml` will be missing parameters for ions in your system.
 
-.. warning::
-   The updated Lipid21 lipid force field is not yet supported in this port of
-   Amber19, as it makes use of Amber features not yet supported in
-   `ParmEd <https://github.com/parmed/parmed>`_.  Amber19 should be preferred
-   over Amber14 for simulations not requiring a lipid force field, but Amber14
-   should be used if the Lipid17 force field is desired.  Alternatively, to use
-   Amber19 with Lipid21, you can prepare your system with AmberTools_ before
-   loading it into OpenMM, as described in Section :numref:`using_amber_files`.
-
 The converted parameter sets come from the `AmberTools 24 release <http://ambermd.org/AmberTools.php>`_
 and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
 
diff --git a/wrappers/python/openmm/app/data/amber19-all.xml b/wrappers/python/openmm/app/data/amber19-all.xml
index 6509f82400..87cb5d305f 100644
--- a/wrappers/python/openmm/app/data/amber19-all.xml
+++ b/wrappers/python/openmm/app/data/amber19-all.xml
@@ -2,4 +2,5 @@
  <Include file="amber19/protein.ff19SB.xml"/>
  <Include file="amber19/DNA.OL21.xml"/>
  <Include file="amber14/RNA.OL3.xml"/>
+ <Include file="amber19/lipid21.xml"/>
 </ForceField>
diff --git a/wrappers/python/openmm/app/data/amber19/lipid21.xml b/wrappers/python/openmm/app/data/amber19/lipid21.xml
new file mode 100644
index 0000000000..eaaa768255
--- /dev/null
+++ b/wrappers/python/openmm/app/data/amber19/lipid21.xml
@@ -0,0 +1,10312 @@
+<ForceField>
+  <Info>
+    <DateGenerated>2025-07-15</DateGenerated>
+    <Source Source="leaprc.lipid21" md5hash="e1c09d4e068913ba25e685b6887f50e3" sourcePackage="AmberTools" sourcePackageVersion="24.8">leaprc.lipid21</Source>
+    <Reference>Dickson, C.J.; Walker, R.C.; Gould, I.R. Lipid21: Complex Lipid Membrane Simulations with AMBER. J. Chem. Theory Comput., 2022, 18, 1726-1736.</Reference>
+  </Info>
+  <AtomTypes>
+    <Type element="C" name="cA" class="cA" mass="12.01" />
+    <Type element="C" name="cB" class="cB" mass="12.01" />
+    <Type element="C" name="cC" class="cC" mass="12.01" />
+    <Type element="C" name="cD" class="cD" mass="12.01" />
+    <Type element="H" name="hA" class="hA" mass="1.008" />
+    <Type element="H" name="hB" class="hB" mass="1.008" />
+    <Type element="H" name="hE" class="hE" mass="1.008" />
+    <Type element="H" name="hL" class="hL" mass="1.008" />
+    <Type element="H" name="hN" class="hN" mass="1.008" />
+    <Type element="H" name="hO" class="hO" mass="1.008" />
+    <Type element="H" name="hX" class="hX" mass="1.008" />
+    <Type element="N" name="nA" class="nA" mass="14.01" />
+    <Type element="N" name="nN" class="nN" mass="14.01" />
+    <Type element="O" name="oC" class="oC" mass="16.0" />
+    <Type element="O" name="oH" class="oH" mass="16.0" />
+    <Type element="O" name="oO" class="oO" mass="16.0" />
+    <Type element="O" name="oP" class="oP" mass="16.0" />
+    <Type element="O" name="oS" class="oS" mass="16.0" />
+    <Type element="O" name="oT" class="oT" mass="16.0" />
+    <Type element="P" name="pA" class="pA" mass="30.97" />
+  </AtomTypes>
+  <Residues>
+    <Residue name="DLPC">
+      <Atom charge="0.245262" name="N" type="nA" />
+      <Atom charge="-0.338973" name="C13" type="cA" />
+      <Atom charge="0.17223" name="H13A" type="hX" />
+      <Atom charge="0.17223" name="H13B" type="hX" />
+      <Atom charge="0.17223" name="H13C" type="hX" />
+      <Atom charge="-0.338973" name="C14" type="cA" />
+      <Atom charge="0.17223" name="H14A" type="hX" />
+      <Atom charge="0.17223" name="H14B" type="hX" />
+      <Atom charge="0.17223" name="H14C" type="hX" />
+      <Atom charge="-0.338973" name="C15" type="cA" />
+      <Atom charge="0.17223" name="H15A" type="hX" />
+      <Atom charge="0.17223" name="H15B" type="hX" />
+      <Atom charge="0.17223" name="H15C" type="hX" />
+      <Atom charge="-0.170824" name="C12" type="cA" />
+      <Atom charge="0.136415" name="H12A" type="hX" />
+      <Atom charge="0.136415" name="H12B" type="hX" />
+      <Atom charge="0.166801" name="C11" type="cA" />
+      <Atom charge="0.078534" name="H11A" type="hE" />
+      <Atom charge="0.078534" name="H11B" type="hE" />
+      <Atom charge="1.339721" name="P" type="pA" />
+      <Atom charge="-0.875812" name="O13" type="oP" />
+      <Atom charge="-0.875812" name="O14" type="oP" />
+      <Atom charge="-0.50948" name="O11" type="oT" />
+      <Atom charge="-0.508176" name="O12" type="oT" />
+      <Atom charge="0.017459" name="C1" type="cA" />
+      <Atom charge="0.095591" name="HA" type="hE" />
+      <Atom charge="0.095591" name="HB" type="hE" />
+      <Atom charge="0.281242" name="C2" type="cA" />
+      <Atom charge="0.063253" name="HS" type="hE" />
+      <Atom charge="-0.552948" name="O21" type="oS" />
+      <Atom charge="0.897613" name="C21" type="cC" />
+      <Atom charge="-0.673755" name="O22" type="oC" />
+      <Atom charge="-0.172159" name="C22" type="cD" />
+      <Atom charge="0.054419" name="H2R" type="hL" />
+      <Atom charge="0.054419" name="H2S" type="hL" />
+      <Atom charge="0.196939" name="C3" type="cA" />
+      <Atom charge="0.070469" name="HX" type="hE" />
+      <Atom charge="0.070469" name="HY" type="hE" />
+      <Atom charge="-0.575489" name="O31" type="oS" />
+      <Atom charge="0.910403" name="C31" type="cC" />
+      <Atom charge="-0.671566" name="O32" type="oC" />
+      <Atom charge="-0.172159" name="C32" type="cD" />
+      <Atom charge="0.054419" name="H2X" type="hL" />
+      <Atom charge="0.054419" name="H2Y" type="hL" />
+      <Atom charge="0.00151" name="C23" type="cD" />
+      <Atom charge="0.019108" name="H3R" type="hL" />
+      <Atom charge="0.019108" name="H3S" type="hL" />
+      <Atom charge="-0.024078" name="C24" type="cD" />
+      <Atom charge="0.02058" name="H4R" type="hL" />
+      <Atom charge="0.02058" name="H4S" type="hL" />
+      <Atom charge="-0.015735" name="C25" type="cD" />
+      <Atom charge="0.009551" name="H5R" type="hL" />
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+      <Bond atomName1="C1" atomName2="HB" />
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+    <Proper class1="cB" class2="cD" class3="cB" class4="hB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cA" class2="cA" class3="cA" class4="cA" periodicity1="3" phase1="0.0" k1="0.75312" periodicity2="2" phase2="3.141592653589793" k2="1.046" periodicity3="1" phase3="3.141592653589793" k3="0.8368000000000001" />
+    <Proper class1="cA" class2="cA" class3="cA" class4="cD" periodicity1="3" phase1="0.0" k1="0.75312" periodicity2="2" phase2="3.141592653589793" k2="1.046" periodicity3="1" phase3="3.141592653589793" k3="0.8368000000000001" />
+    <Proper class1="cA" class2="cA" class3="cD" class4="cD" periodicity1="3" phase1="0.0" k1="0.75312" periodicity2="2" phase2="3.141592653589793" k2="1.046" periodicity3="1" phase3="3.141592653589793" k3="0.8368000000000001" />
+    <Proper class1="cA" class2="cD" class3="cD" class4="cD" periodicity1="3" phase1="0.0" k1="0.75312" periodicity2="2" phase2="3.141592653589793" k2="1.046" periodicity3="1" phase3="3.141592653589793" k3="0.8368000000000001" />
+    <Proper class1="cA" class2="cA" class3="cA" class4="hA" periodicity1="3" phase1="0.0" k1="0.66944" />
+    <Proper class1="cD" class2="cA" class3="cA" class4="hA" periodicity1="3" phase1="0.0" k1="0.66944" />
+    <Proper class1="cA" class2="cA" class3="cD" class4="hL" periodicity1="3" phase1="0.0" k1="0.66944" />
+    <Proper class1="hA" class2="cA" class3="cA" class4="hA" periodicity1="3" phase1="0.0" k1="0.6276" />
+    <Proper class1="hA" class2="cA" class3="cD" class4="hL" periodicity1="3" phase1="0.0" k1="0.6276" />
+    <Proper class1="cD" class2="cD" class3="cA" class4="hA" periodicity1="3" phase1="0.0" k1="0.66944" />
+    <Proper class1="cA" class2="cD" class3="cD" class4="hL" periodicity1="3" phase1="0.0" k1="0.66944" />
+    <Proper class1="cA" class2="cA" class3="cB" class4="cA" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cA" class2="cB" class3="cB" class4="hB" periodicity1="2" phase1="3.141592653589793" k1="27.823600000000003" />
+    <Proper class1="hA" class2="cA" class3="cB" class4="hB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cA" class2="cA" class3="cB" class4="hB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cB" class2="cA" class3="cA" class4="hA" periodicity1="3" phase1="0.0" k1="0.6510304" />
+    <Proper class1="cB" class2="cA" class3="cA" class4="oH" periodicity1="3" phase1="0.0" k1="0.6510304" />
+    <Proper class1="cB" class2="cB" class3="cA" class4="hA" periodicity1="3" phase1="3.141592653589793" k1="1.58992" periodicity2="1" phase2="0.0" k2="4.811599999999999" />
+    <Proper class1="hA" class2="cA" class3="cA" class4="oH" periodicity1="3" phase1="0.0" k1="0.0" periodicity2="1" phase2="0.0" k2="1.046" />
+    <Proper class1="cA" class2="cB" class3="cA" class4="hA" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="hA" class2="cA" class3="cA" class4="hE" periodicity1="3" phase1="0.0" k1="0.6510304" />
+    <Proper class1="cB" class2="cA" class3="cA" class4="hE" periodicity1="3" phase1="0.0" k1="0.6510304" />
+    <Proper class1="cA" class2="cA" class3="nN" class4="cC" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cA" class2="cA" class3="nN" class4="hN" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cA" class2="nN" class3="cC" class4="cD" periodicity1="2" phase1="3.141592653589793" k1="10.46" />
+    <Proper class1="cA" class2="nN" class3="cC" class4="oC" periodicity1="2" phase1="3.141592653589793" k1="10.46" />
+    <Proper class1="cB" class2="cA" class3="cA" class4="nN" periodicity1="3" phase1="0.0" k1="10.0416" periodicity2="2" phase2="3.141592653589793" k2="5.4392000000000005" periodicity3="1" phase3="1.0471975511965976" k3="1.6736000000000002" />
+    <Proper class1="cC" class2="nN" class3="cA" class4="hE" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cD" class2="cC" class3="nN" class4="hN" periodicity1="2" phase1="3.141592653589793" k1="10.46" />
+    <Proper class1="cD" class2="cD" class3="cC" class4="nN" periodicity1="2" phase1="3.141592653589793" k1="0.0" />
+    <Proper class1="hE" class2="cA" class3="cA" class4="nN" periodicity1="3" phase1="0.0" k1="0.6527040000000001" />
+    <Proper class1="hE" class2="cA" class3="nN" class4="hN" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="hL" class2="cD" class3="cC" class4="nN" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="hN" class2="nN" class3="cC" class4="oC" periodicity1="2" phase1="3.141592653589793" k1="10.46" />
+    <Proper class1="nN" class2="cA" class3="cA" class4="oH" periodicity1="3" phase1="0.0" k1="0.6527040000000001" />
+    <Proper class1="nN" class2="cA" class3="cA" class4="oT" periodicity1="3" phase1="0.0" k1="0.0" />
+    <Proper class1="cB" class2="cA" class3="oH" class4="hO" periodicity1="3" phase1="0.0" k1="0.66944" periodicity2="1" phase2="0.0" k2="1.046" />
+    <Proper class1="cB" class2="cB" class3="cA" class4="oH" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="hE" class2="cA" class3="cB" class4="cB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="hE" class2="cA" class3="cB" class4="hB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="oH" class2="cA" class3="cB" class4="hB" periodicity1="2" phase1="0.0" k1="0.0" />
+    <Proper class1="cC" class2="cD" class3="cD" class4="cB" periodicity1="3" phase1="0.0" k1="0.6510304" />
+    <Improper class1="cB" class2="cA" class3="cA" class4="cB" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="cB" class2="cA" class3="cB" class4="hB" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="nN" class2="cA" class3="cC" class4="hN" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="cC" class2="cA" class3="oO" class4="oO" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="cB" class2="cB" class3="cD" class4="hB" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="cC" class2="cD" class3="nN" class4="oC" periodicity1="2" phase1="3.141592653589793" k1="4.6024" />
+    <Improper class1="cC" class2="cD" class3="oC" class4="oS" periodicity1="2" phase1="3.141592653589793" k1="43.932" />
+  </PeriodicTorsionForce>
+  <NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
+    <UseAttributeFromResidue name="charge" />
+    <Atom class="cA" sigma="0.3399669508423535" epsilon="0.4577296" />
+    <Atom class="cB" sigma="0.3399669508423535" epsilon="0.359824" />
+    <Atom class="cC" sigma="0.3399669508423535" epsilon="0.359824" />
+    <Atom class="cD" sigma="0.3399669508423535" epsilon="0.4577296" />
+    <Atom class="hA" sigma="0.2649532787749369" epsilon="0.06568879999999999" />
+    <Atom class="hB" sigma="0.22272467953508485" epsilon="0.029288" />
+    <Atom class="hE" sigma="0.2471353044121301" epsilon="0.06568879999999999" />
+    <Atom class="hL" sigma="0.26014242569697904" epsilon="0.04184" />
+    <Atom class="hN" sigma="0.10690784617684071" epsilon="0.06568879999999999" />
+    <Atom class="hO" sigma="0.10690784617684071" epsilon="0.06568879999999999" />
+    <Atom class="hX" sigma="0.19599771799087468" epsilon="0.06568879999999999" />
+    <Atom class="nA" sigma="0.3249998523775958" epsilon="0.7112800000000001" />
+    <Atom class="nN" sigma="0.3249998523775958" epsilon="0.7112800000000001" />
+    <Atom class="oC" sigma="0.2959921901149463" epsilon="0.87864" />
+    <Atom class="oH" sigma="0.3066473387839048" epsilon="0.8803136" />
+    <Atom class="oO" sigma="0.2959921901149463" epsilon="0.87864" />
+    <Atom class="oP" sigma="0.2959921901149463" epsilon="0.87864" />
+    <Atom class="oS" sigma="0.3000012343465779" epsilon="0.7112800000000001" />
+    <Atom class="oT" sigma="0.3000012343465779" epsilon="0.7112800000000001" />
+    <Atom class="pA" sigma="0.37417746161894255" epsilon="0.8368000000000001" />
+  </NonbondedForce>
+  <Script>
+import openmm
+import openmm.unit
+
+scee_table = {
+}
+scnb_table = {
+    ('cD', 'cD', 'cD', 'cD'): 6.0,
+}
+
+atom_types = [data.atomType[atom] for atom in data.atoms]
+overridden_pairs = {}
+for atom_1, atom_2, atom_3, atom_4 in data.propers:
+    types_key = (atom_types[atom_1], atom_types[atom_2], atom_types[atom_3], atom_types[atom_4])
+    pairs_key = (min(atom_1, atom_4), max(atom_1, atom_4))
+    if types_key in scee_table:
+        overridden_pairs.setdefault(pairs_key, [1.2, 2.0])[0] = scee_table[types_key]
+    if types_key in scnb_table:
+        overridden_pairs.setdefault(pairs_key, [1.2, 2.0])[1] = scnb_table[types_key]
+
+for force in sys.getForces():
+    if isinstance(force, openmm.NonbondedForce):
+        charges, sigmas, epsilons = zip(*(force.getParticleParameters(index) for index in range(force.getNumParticles())))
+        for index in range(force.getNumExceptions()):
+            atom_1, atom_4, charge_prod, sigma, epsilon = force.getExceptionParameters(index)
+            if charge_prod or epsilon:
+                pairs_key = (min(atom_1, atom_4), max(atom_1, atom_4))
+                if pairs_key in overridden_pairs:
+                    scee, scnb = overridden_pairs[pairs_key]
+                    force.setExceptionParameters(index, atom_1, atom_4, charges[atom_1] * charges[atom_4] / scee, (sigmas[atom_1] + sigmas[atom_4]) / 2, openmm.unit.sqrt(epsilons[atom_1] * epsilons[atom_4]) / scnb)
+</Script>
+</ForceField>
\ No newline at end of file