def testAddCharmmPsf(self):
""" Test adding CHARMM PSF file to ParmList """
parms = ParmList()
ala3 = CharmmPsfFile(get_fn('ala3_solv.psf'))
aaa = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
xaaa = CharmmPsfFile(get_fn('ala_ala_ala.psf.xplor'))
aaaa = CharmmPsfFile(get_fn('ala_ala_ala_autopsf.psf'))
parms.add_parm(ala3)
parms.add_parm(aaa)
parms.add_parm(xaaa)
parms.add_parm(aaaa)
# Check indexing
self.assertIs(parms[0], ala3)
self.assertIs(parms[1], aaa)
self.assertIs(parms[2], xaaa)
self.assertIs(parms[3], aaaa)
# Test name indexing
self.assertIs(parms[get_fn('ala3_solv.psf')], ala3)
self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa)
self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa)
self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa)
# Check that the last parm added is active
self.assertIs(parms.parm, parms[-1])
# Set a new active topology
parms.set_new_active(0)
self.assertIs(parms.parm, ala3)
parms.set_new_active(get_fn('ala_ala_ala.psf'))
self.assertIs(parms.parm, aaa)
def parse(filename):
""" Read a CHARMM- or XPLOR-style PSF file
Parameters
----------
filename : str
Name of the file to parse
Returns
-------
psf_file : :class:`CharmmPsfFile`
The PSF file instance with all information loaded
"""
return CharmmPsfFile(filename)
from chemistry import unit as u
from copy import copy
from math import sqrt
import unittest
import warnings
import utils
get_fn = utils.get_fn
skipIf = utils.skipIf
# Suppress warning output from bad psf file... sigh.
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
if has_openmm:
# System
charmm_gas = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
charmm_gas_crds = PDBFile(get_fn('ala_ala_ala.pdb'))
charmm_solv = CharmmPsfFile(get_fn('dhfr_cmap_pbc.psf'))
charmm_solv_crds = CharmmCrdFile(get_fn('dhfr_min_charmm.crd'))
charmm_nbfix = CharmmPsfFile(get_fn('ala3_solv.psf'))
charmm_nbfix_crds = CharmmCrdFile(get_fn('ala3_solv.crd'))
# Parameter sets
param22 = CharmmParameterSet(get_fn('top_all22_prot.inp'),
get_fn('par_all22_prot.inp'))
param36 = CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('toppar_water_ions.str'))
# Make sure all precisions are double
for i in range(mm.Platform.getNumPlatforms()):
plat = mm.Platform.getPlatform(i)
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
from chemistry.openmm.reporters import StateDataReporter
from chemistry import unit as u
# Load the CHARMM files
print('Loading CHARMM files...')
params = CharmmParameterSet('toppar/par_all36_prot.prm',
'toppar/toppar_water_ions.str')
ala2_solv = CharmmPsfFile('ala2_charmmgui.psf')
ala2_crds = CharmmCrdFile('ala2_charmmgui.crd')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Compute the box dimensions from the coordinates and set the box lengths (only
# orthorhombic boxes are currently supported in OpenMM)
coords = ala2_crds.positions
min_crds = [coords[0][0], coords[0][1], coords[0][2]]
max_crds = [coords[0][0], coords[0][1], coords[0][2]]
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
from chemistry.openmm import StateDataReporter
from chemistry import unit as u
# Load the CHARMM files
print('Loading CHARMM files...')
params = CharmmParameterSet('toppar/par_all36_prot.prm')
ala5_gas = CharmmPsfFile('ala5_autopsf.psf')
ala5_crds = app.PDBFile('ala5_autopsf.pdb')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(params, nonbondedMethod=app.NoCutoff,
constraints=app.HBonds, implicitSolvent=app.HCT,
implicitSolventSaltConc=0.1*u.moles/u.liter,
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
from chemistry.amber.openmmreporters import StateDataReporter
from chemistry import unit as u
# Load the CHARMM files
print('Loading CHARMM files...')
params = CharmmParameterSet('toppar/par_all36_prot.prm',
'toppar/toppar_water_ions.str')
ala2_solv = CharmmPsfFile('ala2_charmmgui.psf')
ala2_crds = CharmmCrdFile('ala2_charmmgui.crd')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Compute the box dimensions from the coordinates and set the box lengths (only
# orthorhombic boxes are currently supported in OpenMM)
coords = ala2_crds.positions
min_crds = [coords[0][0], coords[0][1], coords[0][2]]
max_crds = [coords[0][0], coords[0][1], coords[0][2]]
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
from chemistry.openmm import StateDataReporter
from chemistry import unit as u
# Load the CHARMM files
print('Loading CHARMM files...')
params = CharmmParameterSet('toppar/par_all36_prot.prm')
ala5_gas = CharmmPsfFile('ala5_autopsf.psf')
ala5_crds = app.PDBFile('ala5_autopsf.pdb')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(
params,
nonbondedMethod=app.NoCutoff,
