Created using Colab

Protein+Membranes.ipynb

@@ -85,7 +85,7 @@
         "    \"pip -q install py3Dmol\",\n",
         "    \"pip install git+https://github.com/pablo-arantes/biopandas\",\n",
         "    \"pip install git+https://github.com/amber-md/pytraj\",\n",
-        "    \"mamba install openmm=7.7.0\",\n",
+        "    \"mamba install openmm\",\n",
         "    \"mamba install openmmforcefields -c conda-forge -y\",\n",
         "    \"pip install --upgrade MDAnalysis==2.4.2\",\n",
         "    \"mamba install -c conda-forge pdbfixer -y\",\n",
@@ -358,7 +358,7 @@
         "\n",
         "#@markdown **Parameters to generate the protein topology:**\n",
         "\n",
-        "Force_field = \"AMBER14SB\" #@param [\"AMBER14SB\", \"AMBER99SB\", \"AMBER99SB-ILDN\"]\n",
+        "Force_field = \"AMBER99SB\" #@param [\"AMBER14SB\", \"AMBER99SB\", \"AMBER99SB-ILDN\"]\n",
         "Water_type = \"TIP3P\" #@param [\"TIP3P\", \"SPC/E\"]\n",
         "\n",
         "#@markdown The size of the membrane and water box are determined by the minimumPadding argument. All pre-existing atoms are guaranteed to be at least this far from any edge of the periodic box. In particular, it only adds whole copies of the pre-equilibrated membrane patch, so the box dimensions will always be integer multiples of the patch size.\n",
@@ -716,7 +716,8 @@
         "#     simulation.context.setPeriodicBoxVectors(*modeller.boxVectors)\n",
         "\n",
         "print(\"\\t- Energy minimization: \" + str(Minimization_steps) + \" steps\")\n",
-        "simulation.minimizeEnergy(tolerance=10*kilojoule/(nanometer*mole), maxIterations=int(Minimization_steps))\n",
+        "simulation.minimizeEnergy(tolerance=10*kilojoule/mole/nanometer, maxIterations=int(Minimization_steps))\n",
+        "\n",
         "print(\"\\t-> Potential Energy = \" + str(simulation.context.getState(getEnergy=True).getPotentialEnergy()))\n",
         "\n",
         "print(\"\\t- Setting initial velocities...\")\n",