Update OpenFold notebook to updated pytorch2 commit

notebooks/OpenFold.ipynb

@@ -107,11 +107,11 @@
         "\n",
         "python_version = f\"{version_info.major}.{version_info.minor}\"\n",
         "\n",
-        "\n",
-        "os.system(\"wget -qnc https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\")\n",
-        "os.system(\"bash Mambaforge-Linux-x86_64.sh -bfp /usr/local\")\n",
+        "os.system(\"wget -qnc https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh\")\n",
+        "os.system(\"bash Miniforge3-Linux-x86_64.sh -bfp /usr/local\")\n",
+        "os.environ[\"PATH\"] = \"/usr/local/bin:\" + os.environ[\"PATH\"]\n",
         "os.system(\"mamba config --set auto_update_conda false\")\n",
-        "os.system(f\"mamba install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=7.7.0 python={python_version} pdbfixer biopython=1.83\")\n",
+        "os.system(f\"mamba install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=8.2.0 python={python_version} pdbfixer biopython=1.83\")\n",
         "os.system(\"pip install -q torch ml_collections py3Dmol modelcif\")\n",
         "\n",
         "try:\n",
@@ -127,7 +127,7 @@
         "\n",
         "    %shell mkdir -p /content/openfold/openfold/resources\n",
         "\n",
-        "    commit = \"3bec3e9b2d1e8bdb83887899102eff7d42dc2ba9\"\n",
+        "    commit = \"1ffd197489aa5f35a5fbce1f00d7dd49bce1bd2f\"\n",
         "    os.system(f\"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}\")\n",
         "\n",
         "    os.system(f\"cp -f -p /content/stereo_chemical_props.txt /usr/local/lib/python{python_version}/site-packages/openfold/resources/\")\n",
@@ -893,8 +893,7 @@
   "metadata": {
     "colab": {
       "provenance": [],
-      "gpuType": "T4",
-      "toc_visible": true
+      "gpuType": "T4"
     },
     "kernelspec": {
       "display_name": "Python 3",
@@ -907,4 +906,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}
\ No newline at end of file