folding viroporin related.ipynb

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       "_ColormakerRegistry()"
      ]
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    }
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   "source": [
    "# Initially with openmm\n",
    "#!/usr/bin/env python3\n",
    "from simtk.openmm.app import *\n",
    "from simtk.openmm import *\n",
    "from simtk.unit import *\n",
    "from sys import stdout\n",
    "import os\n",
    "import sys\n",
    "import argparse\n",
    "import nglview as nv\n",
    "import pytraj as pt\n",
    "import pdbfixer"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Easiest way to fix downloaded PDB files to be processed by OpenMM is to run pdbfixer from the command line and use the HTML interface that shows up.\n",
    "Easy as pie!\n",
    "Ref: https://htmlpreview.github.io/?https://raw.github.com/pandegroup/pdbfixer/master/Manual.html\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<Topology; 8 chains, 166 residues, 2342 atoms, 2316 bonds>\n"
     ]
    }
   ],
   "source": [
    "#pdb= PDBFile('data/6lvn.pdb')\n",
    "pdb = PDBFile('data/6lvn_fixed.pdb')\n",
    "forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n",
    "modeller = Modeller(pdb.topology, pdb.positions)\n",
    "modeller.addHydrogens(forcefield)\n",
    "print(modeller.topology)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "findPlatform() missing 1 required positional argument: 'kernelNames'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
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      "\u001b[0;31mTypeError\u001b[0m: findPlatform() missing 1 required positional argument: 'kernelNames'"
     ]
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   ],
   "source": [
    "platform = Platform.findPlatform()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "code_folding": []
   },
   "outputs": [],
   "source": [
    "# from https://www.ncbi.nlm.nih.gov/protein/QHD43417/\n",
    "pdb= PDBFile('data/QHD43417.pdb')\n",
    "forcefield = ForceField('amber03.xml', 'amber03_obc.xml')\n",
    "modeller = Modeller(pdb.topology, pdb.positions)\n",
    "#modeller.addHydrogens(forcefield)\n",
    "#print(modeller.topology)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<Topology; 1 chains, 36 residues, 596 atoms, 602 bonds>\n"
     ]
    }
   ],
   "source": [
    "# from https://www.rcsb.org/structure/1vii\n",
    "pdb2 = PDBFile('data/1vii.pdb')\n",
    "\n",
    "forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n",
    "#forcefield = ForceField('amber03.xml', 'amber03_obc.xml')\n",
    "modeller = Modeller(pdb2.topology, pdb2.positions)\n",
    "modeller.addHydrogens(forcefield)\n",
    "print(modeller.topology)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<Topology; 1 chains, 125 residues, 1826 atoms, 1842 bonds>\n"
     ]
    }
   ],
   "source": [
    "# from https://www.rcsb.org/structure/1vii\n",
    "pdb2 = PDBFile('data/2prf.pdb')\n",
    "\n",
    "forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n",
    "#forcefield = ForceField('amber03.xml', 'amber03_obc.xml')\n",
    "modeller = Modeller(pdb2.topology, pdb2.positions)\n",
    "modeller.addHydrogens(forcefield)\n",
    "print(modeller.topology)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "writing every 100 steps\n",
      "#\"Step\",\"Potential Energy (kJ/mole)\",\"Temperature (K)\"\n",
      "1000,-9644.40020582318,270.0506294986803\n",
      "2000,-8680.520795637349,296.1787257108011\n",
      "3000,-9097.036088179564,304.7337254578176\n",
      "4000,-8954.231014715442,301.8824781533834\n",
      "5000,-9346.255330631637,297.89822392555806\n",
      "6000,-9357.570242687116,296.46932742231485\n",
      "7000,-9675.009728839988,301.9894399042805\n",
      "8000,-9703.878662353678,302.96458276900637\n",
      "9000,-9616.550062142593,305.0325355038976\n",
      "10000,-9884.111369013935,305.2985066260844\n",
      "11000,-9566.876458314979,303.2917890009863\n",
      "12000,-9662.805238462446,295.6221499845513\n",
      "13000,-9486.264810641647,298.9411822912113\n",
      "14000,-9865.326300558943,300.5836706081506\n",
      "15000,-9594.967312642337,305.2221492046354\n",
      "16000,-9649.80303714579,299.3665647701112\n",
      "17000,-9940.932724086933,301.43139805947516\n"
     ]
    }
   ],
   "source": [
    "system = forcefield.createSystem(modeller.topology,\n",
    "  implicitSolvent=OBC2,   # matches https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980750/#bib39\n",
    "  nonbondedMethod=NoCutoff, nonbondedCutoff=1*nanometer,\n",
    "  constraints=HBonds)\n",
    "integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 2*femtoseconds)\n",
    "simulation = Simulation(modeller.topology, system, integrator)\n",
    "simulation.context.setPositions(modeller.positions)\n",
    "simulation.minimizeEnergy()\n",
    "\n",
    "steps = 100000\n",
    "steps_write = max(1, steps//1000)\n",
    "print(\"writing every %d steps\" % steps_write)\n",
    "simulation.reporters.append(PDBReporter('output.pdb', 1000))\n",
    "simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,potentialEnergy=True, temperature=True))\n",
    "simulation.step(steps)"
   ]
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   "execution_count": 2,
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   "source": [
    "traj = pt.load('output.pdb')\n",
    "view = nv.show_pytraj(traj)\n",
    "view"
   ]
  },
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   "execution_count": null,
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