Files

Using CHARMM-GUI to embed B2AR in a solvated membrane

  1. Go to CHARMM-GUI’s membrane builder and upload the pdb file. (apo_snapshot.pdb). Select PDB format and click Next Step.
  2. Stick with the default selection (Protein) and click Next Step.
  3. Select Terminal group patching and select termin NTER and CTER.
  4. Select Disulfide bonds for the pairs 184-190 and 106-191 and click Next Step.
  5. Select Align the First Principal Axis Along Z (the suggestion for a homo-oligomer) and click Next Step.
  6. Keep the default selections for Heterogeneous Lipid, Rectangular Box Type, 17.5 water thickness. Select Number of lipid components and select POPC lipids with 55 lipids on the upperleaflet and lowerleaflet. Clike Next Step.
  7. Keep all default selections (Replacement method, check lipid ring (and protein surface) penetration, Include Ions 0.15 KCl and Ion Placing Method: Monte-Carlo. Click Next Step.
  8. Click Next Step to assemble components. When you arrive at Step 5, select OpenMM as the Input generation option. Keep all the other default options (Generate grid information for PME FFT automatically and NPT ensemble. Click Next Step.

B2AR in membrane

Simulating the system in OpenMM

The quick way

From the charmm-gui.tgz extract toppar/ directory and the openmm/ directory. The README file in the openmm/ directory is a csh script to run a standard equilibration and production simulation.

The flexible way

If you want finer control, you can write your own OpenMM code to equilibrate and simulate the system.

OpenMM can directly read CHARMM input files through the use of the simtk.openmm.app application layer. This enables the use of all the powerful setup tools in the CHARMM ecosystem that a user might be familiar with such as the CHARMM-GUI, VMD, CGenFF program (DOI:10.1002/jcc.21367), etc. This allows users who are already working in the CHARMM environment to harness the GPU speeds that OpenMM provides without having to modify their simulation system description files.

OpenMM can also read CHARMM force field files making it is possible to use force fields that aren’t already included in OpenMM such as the general CHARMM force field (CGenFF). For example, a user can generate an str file with the CGenFF program for a ligand and load it into OpenMM. However, when using this feature, the CharmmParameterSet class needs to be used instead of the ForceField class to load all the other CHARMM force field files as demonstrated in the example in Listing 1.

The example demonstrates how to use CHARMMM files that were generated with the CHARMM-GUI in an OpenMM script. The OpenMM app layer includes several classes to load CHARMM files. The CharmmPsfFile class reads the psf file and instantiates a chemical structure on which one can then call the createSystem() method to creates an OpenMM system object. For the atomic coordinates, a regular pdb file can be used or the CharmmCrdFile or CharmmRstFile classes can be used to read CHARMM coordinate files. Files containing force field definitions come in a variety of formats such as prm, par, top, rtf, inp and str. These files are loaded into a CharmmParameterSet object which is then included as the first parameter when createSystem() is called on the chemical structure. For this example, the membrane builder in the CHARMM-GUI was used to generate the input files for the B2AR in a POPC lipid membrane. The membrane builder provides a straightforward way to go from the RCSB X-ray structure to the protein embedded in a membrane with all the relevant CHARMM input files.

from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout, exit, stderr

# Load CHARMM files
psf = CharmmPsfFile('step5_charmm2omm.psf')
pdb = PDBFile('step5_charmm2omm.pdb')
params = CharmmPsfFile('par_all36_prot.rtf', 'top_all36_prot.prm',
                       'par_all36_lipid.rtf', 'top_all36_lipid.prm',
                       'toppar_water_ion.str')

# Create an openmm system by calling createSystem on psf
system = psf.createSystem(params, nonbondedMethod=NoCutoff,
         nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin,   # Temperature of head bath
                                1/picosecond, # Friction coefficient
                                0.002*picoseconds) # Time step

simulation = Simulation(psf.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()

# Set up the reporters to report energies every 1000 steps.
simulaiton.reporters.append(PDBReporter('output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
                            potentialEnergy=True, temperature=True))
# run simulation
simulation.step(10000)

The CHARMM-GUI also generates a more elaborate set of OpenMM scripts to run equilibration and the production simulation that are very straightforward to use (see “The quick way” above). When OpenMM is selected in the last step, CHARMM-GUI provides all the relevant OpenMM scripts in the downloaded tarball. The parameters and arguments for OpenMM objects and functions are provided in the inp files for all equilibration steps and production. This makes it simple to change parameters such as the time-step or electrostatic cut-off method.