Update BRD4 notebook

openforcefield · Sep 3, 2024 · 4dcd398 · 4dcd398
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diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/.gitignore b/examples/using_smirnoff_with_amber_protein_forcefield/.gitignore
@@ -1,4 +1,5 @@
 complex.*
+complex_pointenergy.mdp
 receptor.*
 ligand.*
 protein.pdb
diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb b/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
@@ -24,10 +24,11 @@
     "repo_url = (\n",
     "    \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
     ")\n",
+    "\n",
     "sources = {\n",
-    "    \"receptor.pdb\": repo_url + \"BRD4/pdb/BRD4.pdb\",\n",
-    "    \"ligand.pdb\": repo_url + \"BRD4/pdb/ligand-1.pdb\",\n",
-    "    \"ligand.sdf\": repo_url + \"BRD4/sdf/ligand-1.sdf\",\n",
+    "    \"receptor.pdb\": f\"{repo_url}BRD4/pdb/BRD4.pdb\",\n",
+    "    \"ligand.pdb\": f\"{repo_url}BRD4/pdb/ligand-1.pdb\",\n",
+    "    \"ligand.sdf\": f\"{repo_url}BRD4/sdf/ligand-1.sdf\",\n",
     "}\n",
     "for filename, url in sources.items():\n",
     "    r = requests.get(url)\n",
@@ -40,44 +41,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from openff.toolkit import ForceField, Molecule, Topology"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Later we will use `Interchange.__add__`, which is an experimental feature. It needs to be turned on by setting the environment variable below, and by doing so we accept [some stability and accuracy risks](https://docs.openforcefield.org/projects/interchange/en/stable/using/experimental.html)."
+    "from openff.toolkit import ForceField, Molecule, Quantity, Topology"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "env: INTERCHANGE_EXPERIMENTAL=1\n"
-     ]
-    }
-   ],
-   "source": [
-    "%env INTERCHANGE_EXPERIMENTAL=1"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
    "metadata": {
     "tags": []
    },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "2f3b86c392c24705b86721395cf43ea4",
+       "model_id": "48226cb62a2849029c42d579843ef0f7",
        "version_major": 2,
        "version_minor": 0
       },
@@ -90,8 +67,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/_experimental.py:35: UserWarning: Interchange object combination is experimental and likely to produce strange results. Any workflow using this method is not guaranteed to be suitable for production. Use with extreme caution and thoroughly validate results!\n",
-      "  return func(*args, **kwargs)\n"
+      "/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/interchange/operations/_combine.py:52: InterchangeCombinationWarning: Interchange object combination is complex and likely to produce strange results outside of a limited set of use cases it has been tested in. Any workflow using this method is not guaranteed to be suitable for production or stable between versions. Use with extreme caution and thoroughly validate results!\n",
+      "  warnings.warn(\n"
      ]
     }
    ],
@@ -107,32 +84,32 @@
     "\n",
     "receptor = ff14sb.create_interchange(topology=receptor_topology)\n",
     "\n",
-    "complex_system = receptor.combine(ligand)\n",
-    "\n",
-    "# TODO\n",
-    "# complex.box = pdbfile box vectors ...\n",
-    "# complex.positions = np.vstack([receptor.positions, ligand.positions])"
+    "# Interchange.combine works nicely for some cases but hasn't been tested for all - use caution\n",
+    "# if adapting this for more novel workflows!\n",
+    "complex_system = receptor.combine(ligand)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to OpenMM"
+    "### Export to OpenMM\n",
+    "\n",
+    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#openmm) for more options."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14380adf0> >"
+       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14ba376f0> >"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -147,31 +124,35 @@
     "tags": []
    },
    "source": [
-    "### Export to Amber"
+    "### Export to Amber\n",
+    "\n",
+    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#amber) for more options."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# TODO: Fix inferring residue information with mixed topology\n",
-    "if False:\n",
-    "    complex_system.to_inpcrd(\"complex.inpcrd\")\n",
-    "    complex_system.to_prmtop(\"complex.prmtop\")"
+    "complex_system.to_inpcrd(\"complex.inpcrd\")\n",
+    "complex_system.to_prmtop(\"complex.prmtop\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Export to GROMACS"
+    "### Export to GROMACS\n",
+    "\n",
+    "See [docs](https://docs.openforcefield.org/projects/interchange/en/stable/using/output.html#gromacs) for more options.\n",
+    "\n",
+    "GROMACS does not support vacuum simulations. In this example, we didn't add solvent and the original PDB file didn't have box vectors. We'll just arbitrarily add a 4 nm cubic box around the receptor-ligand complex."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {
     "tags": []
    },
@@ -180,14 +161,16 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/interop/gromacs/export/_export.py:48: UserWarning: WARNING: System defined with no box vectors, which GROMACS does not offically support in versions 2020 or newer (see https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5  nm cube.\n",
-      "  self._write_gro(gro, decimal)\n"
+      "/Users/mattthompson/micromamba/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/interchange/components/mdconfig.py:471: UserWarning: Ambiguous failure while processing constraints. Constraining h-bonds as a stopgap.\n",
+      "  warnings.warn(\n"
      ]
     }
    ],
    "source": [
-    "complex_system.to_gro(\"complex.gro\")\n",
-    "complex_system.to_top(\"complex.top\")"
+    "complex_system.box = Quantity([4, 4, 4], \"nanometer\")\n",
+    "\n",
+    "# This step might be slow, writing some large proteins is not yet optimized\n",
+    "complex_system.to_gromacs(\"complex\")"
    ]
   }
  ],
@@ -208,7 +191,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,