Created using Colab

pablo-arantes · Jan 22, 2025 · f8c232b · f8c232b
1 parent 6842417
commit f8c232b
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/Protein_ligand.ipynb b/Protein_ligand.ipynb
@@ -133,13 +133,12 @@
         "import pytraj as pt\n",
         "subprocess.run(\"pip -q install py3Dmol\", shell=True)\n",
         "subprocess.run(\"pip install git+https://github.com/pablo-arantes/biopandas\", shell=True)\n",
-        "subprocess.run(\"mamba install openmm=7.7.0 pdbfixer -y\", shell=True)\n",
+        "subprocess.run(\"mamba install openmm pdbfixer -y\", shell=True)\n",
         "subprocess.run(\"mamba install openmmforcefields -c conda-forge -y\", shell=True)\n",
         "subprocess.run(\"pip install prolif==1.1.0\", shell=True)\n",
         "subprocess.run(\"mamba install -c conda-forge openbabel -y\", shell=True)\n",
         "subprocess.run(\"mamba install -c conda-forge parmed -y\", shell=True)\n",
         "subprocess.run(\"pip install --upgrade MDAnalysis==2.4.2\", shell=True)\n",
-        "subprocess.run(\"pip install numpy==1.23.5\", shell=True)\n",
         "\n",
         "#load dependencies\n",
         "from openmm import app, unit\n",
@@ -1271,7 +1270,8 @@
         "    simulation.context.setPeriodicBoxVectors(*inpcrd.boxVectors)\n",
         "\n",
         "print(\"\\t- Energy minimization: \" + str(Minimization_steps) + \" steps\")\n",
-        "simulation.minimizeEnergy(tolerance=10*kilojoule/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",