Typo in the beta-2-adrenergic receptor tutorial

[DanielWicz]

In the tutorial here: http://openmm.org/tutorials/b2ar_membrane/
I think in the line

params = CharmmPsfFile('par_all36_prot.rtf', 'top_all36_prot.prm',
                       'par_all36_lipid.rtf', 'top_all36_lipid.prm',
                       'toppar_water_ion.str')

it should be

params = CharmmParameterSet('par_all36_prot.rtf', 'top_all36_prot.prm',
                            'par_all36_lipid.rtf', 'top_all36_lipid.prm',
                            'toppar_water_ion.str')

[DanielWicz]

Plus there's more errors. Topology files are named like parameter files and vice-versa. Is there this tutorial on the GitHub repo ?

[apayne97]

I just did this for my own membrane protein, and I'll just show what I had here:

(i used the charmm36m forcefield, which changed the name of the par_all36_prot.prm file)
param_file_names = [
'top_all36_prot.rtf',
'par_all36m_prot.prm',
'top_all36_lipid.rtf',
'par_all36_lipid.prm',
'toppar_water_ions.str',
]

You're not alone! thankfully easily discovered by comparing the file names but an unnecessary typo nonetheless.

[apayne97]

for future reference I'll include the code represented in the tutorial here:

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)

Another typo: simulaiton.reporters.append(PDBReporter('output.pdb', 1000)) should be simulation.reporters.append(PDBReporter('output.pdb', 1000))

And probably more importantly, this current tutorial results in a system without unit cell dimensions, so periodic methods like PME cannot be used. The 'NoCutoff' nonbondedMethod is not ideal and there are some better tools now to use. In light of all of this, and with @jchodera's suggestion, I've made a new issue #3152 to work on an updated guide / tutorial for simulating systems set up in CHARMM-GUI.