diff --git a/Protein+Membranes.ipynb b/Protein+Membranes.ipynb index 154e513..51fbb67 100644 --- a/Protein+Membranes.ipynb +++ b/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",