Created using Colab

pablo-arantes · Jan 22, 2025 · e231cbd · e231cbd
1 parent 20ea0c0
commit e231cbd
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/AlphaFold2+MD.ipynb b/AlphaFold2+MD.ipynb
@@ -200,7 +200,7 @@
         "subprocess.run(\"rm -rf /usr/local/conda-meta/pinned\", shell=True)\n",
         "subprocess.run(\"mamba install -c conda-forge ambertools -y\", shell=True)\n",
         "import pytraj as pt\n",
-        "os.system(f\"mamba install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=7.7.0 pdbfixer 2>&1 1>/dev/null\")\n",
+        "os.system(f\"mamba install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm pdbfixer 2>&1 1>/dev/null\")\n",
         "os.system(\"touch HH_READY\")\n",
         "os.system(\"touch AMBER_READY\")\n",
         "os.system(\"pip install --upgrade MDAnalysis==2.4.2\")\n",
@@ -1334,7 +1334,8 @@
         "    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",