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Protein_ligand.ipynb

@@ -142,11 +142,10 @@
         "!bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n",
         "!rm -r Miniconda3-latest-Linux-x86_64.sh /content/ProLIF prolif.sh\n",
         "!conda install -y -q -c conda-forge openmm=7.6 python=3.8 pdbfixer 2>&1 1>/dev/null\n",
+        "!conda install -c conda-forge openbabel --yes 2>&1 1>/dev/null\n",
         "!conda install -c conda-forge ambertools --yes 2>&1 1>/dev/null\n",
         "!conda install -c conda-forge parmed  --yes 2>&1 1>/dev/null\n",
         "!conda install -c conda-forge openff-toolkit --yes 2>&1 1>/dev/null\n",
-        "!conda install -c bioconda pybel --yes\n",
-        "!conda install -c openbabel openbabel --yes\n",
         "\n",
         "#load dependencies\n",
         "sys.path.append('/usr/local/lib/python3.8/site-packages/')\n",
@@ -264,13 +263,13 @@
         "#@title **Please, provide the necessary input files below**: \n",
         "#@markdown **Important:** The protonation of your ligand is crucial for the correct parameterization of the molecule.\n",
         "%%capture\n",
-        "import pybel\n",
         "import rdkit\n",
         "import mdtraj as md\n",
         "from rdkit import Chem\n",
         "from rdkit.Chem import AllChem,Draw\n",
         "from rdkit.Chem.Draw import IPythonConsole\n",
         "from pdbfixer import PDBFixer\n",
+        "from openbabel import pybel\n",
         "\n",
         "Protein_PDB_file_name = 'protein.pdb' #@param {type:\"string\"}\n",
         "Ligand_PDB_file_name = 'ligand.pdb'  #@param {type:\"string\"}\n",