Replace ParmEd with Interchange in Amber/GROMACS example

.github/workflows/examples.yml

@@ -101,6 +101,8 @@ jobs:
       - name: Install package
         shell: bash -l {0}
         run: |
+          pip install git+https://github.com/openforcefield/openff-interchange.git@skip-drivers
+
           # Remove the packaged openff-toolkit, installed as a dependency of openmmforcefields
           conda remove --force openff-toolkit-base
           python setup.py develop --no-deps
@@ -127,6 +129,7 @@ jobs:
             NB_ARGS+=" --ignore=examples/QCArchive_interface"
             NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
             NB_ARGS+=" --ignore=examples/conformer_energies"
+            NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
           fi
           pytest $NB_ARGS examples
 

docs/releasehistory.md

@@ -14,6 +14,12 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
   [`Molecule.to_hill_formula`](openff.toolkit.topology.Molecule.to_hill_formula) is now a class method
   and no longer accepts input of NetworkX graphs.
 
+### Examples added
+
+- [PR #1113](https://github.com/openforcefield/openff-toolkit/pull/1113): Updates the Amber/GROMACS
+  example to use Interchange.
+
+
 ## 0.10.1 Minor feature and bugfix release
 
 ### Behaviors changed and bugfixes

environment.yml

@@ -3,6 +3,7 @@ name: binder-env
 channels:
   - conda-forge
   - defaults
+  - bioconda
 dependencies:
   # Let conda pull in the toolkit and its deps
   - openff-toolkit
@@ -13,3 +14,6 @@ dependencies:
   - qcportal
   - qcengine
   - openmmforcefields
+  - openff-interchange >=0.1.2
+  - gromacs
+  - lammps

examples/environment.yaml

@@ -17,3 +17,7 @@ dependencies:
   - numpy
   - openmm
   - openff-forcefields >=2.0.0
+  - openff-interchange >=0.1.3
+  - gromacs
+  - lammps
+  - ambertools

examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb → examples/using_smirnoff_in_amber_or_gromacs/convert_with_parmed.ipynb

@@ -3,6 +3,17 @@
   {
    "cell_type": "markdown",
    "metadata": {},
+   "source": [
+    " <div class=\"alert alert-block alert-info\">\n",
+    "    <b>Note:</b> \n",
+    "    Please take a look at the other notebook in the folder (<code>export_with_interchange.ipynb</code>), showcasing how to use OpenFF Interchange. Interchange is well-validated for small molecule interoperability with several formats and is in the process of replacing ParmEd in OpenFF workflows.</div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "## Convert Open Forcefield System to AMBER and GROMACS input files\n",
     "\n",
@@ -40,7 +51,8 @@
     "    from simtk.openmm.app import PDBFile\n",
     "\n",
     "from openff.toolkit.topology import Molecule, Topology\n",
-    "from openff.toolkit.typing.engines.smirnoff import ForceField"
+    "from openff.toolkit.typing.engines.smirnoff import ForceField\n",
+    "from openff.toolkit.utils import get_data_file_path"
    ]
   },
   {
@@ -53,7 +65,9 @@
     "cyclohexane = Molecule.from_smiles(\"C1CCCCC1\")\n",
     "\n",
     "# Obtain the OpenMM Topology object from the PDB file.\n",
-    "pdbfile = PDBFile(\"1_cyclohexane_1_ethanol.pdb\")\n",
+    "pdbfile = PDBFile(\n",
+    "    get_data_file_path(\"systems/test_systems/1_cyclohexane_1_ethanol.pdb\")\n",
+    ")\n",
     "omm_topology = pdbfile.topology\n",
     "\n",
     "# Create the Open Forcefield Topology.\n",
@@ -82,7 +96,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true,
+    "tags": []
+   },
    "source": [
     "### Convert OpenMM System to AMBER and GROMACS files\n",
     "\n",
@@ -263,7 +280,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -277,7 +294,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,