Update openmm to 7.7.0, patch not needed anymore, update pdbfixer

71d7bd5d · Vaclav Hanzl · 8b36691f · 71d7bd5d
Commit 71d7bd5d authored May 09, 2023 by Vaclav Hanzl
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notebooks/OpenFold.ipynb notebooks/OpenFold.ipynb +2 -6

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--- a/notebooks/OpenFold.ipynb
+++ b/notebooks/OpenFold.ipynb
@@ -185,12 +185,8 @@
        "    %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
        "    %shell /usr/bin/python3 -m pip install -q ./openfold\n",
        "\n",
-        "    %shell conda install -y -q -c conda-forge openmm=7.5.1\n",
-        "    # Apply OpenMM patch.\n",
-        "    %shell pushd /opt/conda/lib/python{python_version}/site-packages/ && \\\n",
-        "        patch -p0 < /content/openfold/lib/openmm.patch && \\\n",
-        "        popd\n",
-        "    %shell conda install -y -q -c conda-forge pdbfixer=1.7\n",
+        "    %shell conda install -y -q -c conda-forge openmm=7.7.0\n",
+        "    %shell conda install -y -q -c conda-forge pdbfixer\n",
        "\n",
        "    if(weight_set == 'AlphaFold'):\n",
        "      %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",