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Commit 71d7bd5d authored by Vaclav Hanzl's avatar Vaclav Hanzl
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Update openmm to 7.7.0, patch not needed anymore, update pdbfixer

parent 8b36691f
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notebooks/OpenFold.ipynb
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...@@ -185,12 +185,8 @@ ...@@ -185,12 +185,8 @@
" %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n", " %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
" %shell /usr/bin/python3 -m pip install -q ./openfold\n", " %shell /usr/bin/python3 -m pip install -q ./openfold\n",
"\n", "\n",
" %shell conda install -y -q -c conda-forge openmm=7.5.1\n", " %shell conda install -y -q -c conda-forge openmm=7.7.0\n",
" # Apply OpenMM patch.\n", " %shell conda install -y -q -c conda-forge pdbfixer\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",
"\n", "\n",
" if(weight_set == 'AlphaFold'):\n", " if(weight_set == 'AlphaFold'):\n",
" %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n", " %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",
......
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