def testAddAmberParm(self):
""" Test adding AmberParm-derived instances to ParmList """
parms = ParmList()
amber = AmberParm(get_fn('tip4p.parm7'))
chamber = ChamberParm(get_fn('ala_ala_ala.parm7'))
amoeba = AmoebaParm(get_fn('nma.parm7'))
parms.add_parm(amber)
parms.add_parm(chamber)
parms.add_parm(amoeba)
self.assertEqual(len(parms), 3)
# Test int indexing
self.assertIs(parms[0], amber)
self.assertIs(parms[1], chamber)
self.assertIs(parms[2], amoeba)
self.assertRaises(IndexError, lambda: parms[3])
# Test name indexing
self.assertIs(parms[get_fn('tip4p.parm7')], amber)
self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber)
self.assertIs(parms[get_fn('nma.parm7')], amoeba)
self.assertRaises(IndexError, lambda: parms['noparm'])
# Check that the last added parm is active
self.assertIs(parms.parm, amoeba)
# Set a new active topology
parms.set_new_active(0)
self.assertIs(parms.parm, amber)
parms.set_new_active(get_fn('ala_ala_ala.parm7'))
self.assertIs(parms.parm, chamber)
self.assertRaises(IndexError, lambda: parms.set_new_active(3))
self.assertIs(parms.parm, chamber)
def get_rmsd(initparas):
global idxs, mcresids2, atompairs
#Modify the C4 terms in the prmtop file
for i in range(0, len(idxs)):
prmtop.parm_data['LENNARD_JONES_CCOEF'][idxs[i]] = initparas[i]
#Overwrite the prmtop file
prmtop.write_parm('OptC4.top')
#Perform the OpenMM optimization
#Use AmberParm function to transfer the topology and
#coordinate file to the object OpenMM can use
Ambermol = AmberParm('OptC4.top', options.cfile)
# Create the OpenMM system
print('Creating OpenMM System')
if options.simupha == 'gas':
system = Ambermol.createSystem(nonbondedMethod=app.NoCutoff)
elif options.simupha == 'liquid':
system = Ambermol.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8.0*u.angstroms,
constraints=app.HBonds,)
#Add restraints
force = mm.CustomExternalForce("k*((x-x0)^2+(y-y0)^2+(z-z0)^2)")
force.addGlobalParameter("k", 200.0)
force.addPerParticleParameter("x0")
force.addPerParticleParameter("y0")
force.addPerParticleParameter("z0")
#for i in range(0, len(Ambermol.atoms)):
for i, atom_crd in enumerate(Ambermol.positions):
#if (Ambermol.atoms[i].residue.number+1 not in mcresids2) and \
if (i+1 not in mcresids2) and \
(Ambermol.atoms[i].residue.name not in ['WAT', 'HOH']) and \
(Ambermol.atoms[i].name in ['CA', 'C', 'N']):
force.addParticle(i, atom_crd.value_in_unit(u.nanometers))
system.addForce(force)
# Create the integrator to do Langevin dynamics
# Temperature of heat bath, Friction coefficient, Time step
integrator = mm.LangevinIntegrator(300*u.kelvin, 1.0/u.picoseconds,
1.0*u.femtoseconds,)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not
# specify the platform to use the default (fastest) platform
# Create the Simulation object
if options.platf == 'ref':
platform = mm.Platform.getPlatformByName('Reference')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cpu':
platform = mm.Platform.getPlatformByName('CPU')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cuda':
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
elif options.platf == 'opencl':
platform = mm.Platform.getPlatformByName('OpenCL')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
# Set the particle positions
sim.context.setPositions(Ambermol.positions)
# Output the rst file
restrt = RestartReporter(options.rfile, 100, write_velocities=False)
sim.reporters.append(restrt)
# Minimize the energy
print('Minimizing energy ' + str(options.maxsteps) + ' steps.')
sim.minimizeEnergy(maxIterations=options.maxsteps)
# Overwrite the final file
state = sim.context.getState(getPositions=True, enforcePeriodicBox=True)
restrt.report(sim, state)
val_aft_min = []
crds_aft_min = read_rstf(options.rfile)
for i in atompairs:
if len(i) == 2:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
bond = calc_bond(crd1, crd2)
val_aft_min.append(('bond', bond))
elif len(i) == 3:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
crd3 = crds_aft_min[i[2]-1]
angle = calc_angle(crd1, crd2, crd3)
val_aft_min.append(('angle', angle))
elif len(i) == 4:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
crd3 = crds_aft_min[i[2]-1]
crd4 = crds_aft_min[i[3]-1]
dih = calc_dih(crd1, crd2, crd3, crd4)
val_aft_min.append(('dih', dih))
valdiffs = []
for i in range(0, len(atompairs)):
if val_bf_min[i][0] == 'bond':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 100.0
elif val_bf_min[i][0] == 'angle':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 2.0
elif val_bf_min[i][0] == 'dih':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1])
if (360.0 - valdiff < valdiff):
valdiff = 360.0 - valdiff
valdiffs.append(valdiff)
fnldiff = numpy.sum(valdiffs)
print(fnldiff)
return fnldiff
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.amber import AmberParm
from chemistry.openmm.reporters import StateDataReporter, NetCDFReporter
from chemistry import unit as u
# Load the Amber files
print('Loading Amber files...')
ala5_gas = AmberParm('ala5_gas.parm7', 'ala5_gas.rst7')
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds,
implicitSolvent=app.GBn2,
implicitSolventSaltConc=0.1 * u.moles / u.liter,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300 * u.kelvin, # Temperature of heat bath
1.0 / u.picoseconds, # Friction coefficient
2.0 * u.femtoseconds, # Time step
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.amber import AmberParm
from chemistry.openmm.reporters import StateDataReporter, NetCDFReporter
from chemistry import unit as u
# Load the Amber files
print('Loading Amber files...')
ala5_gas = AmberParm('ala5_gas.parm7', 'ala5_gas.rst7')
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(nonbondedMethod=app.NoCutoff,
constraints=app.HBonds, implicitSolvent=app.GBn2,
implicitSolventSaltConc=0.1*u.moles/u.liter,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry.amber import AmberParm
from chemistry.openmm.reporters import StateDataReporter, NetCDFReporter
from chemistry import unit as u
# Load the Amber files
print('Loading AMBER files...')
ala2_solv = AmberParm('ala2_solv.parm7', 'ala2_solv.rst7')
# Create the OpenMM system
print('Creating OpenMM System')
system = ala2_solv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8.0*u.angstroms,
constraints=app.HBonds,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
def get_rmsd(initparas):
global idxs
print(initparas)
#Modify the C4 terms in the prmtop file
for i in range(0, len(idxs)):
prmtop.parm_data['LENNARD_JONES_CCOEF'][idxs[i]] = initparas[i]
#Overwrite the prmtop file
prmtop.write_parm('OptC4.top')
#Perform the OpenMM optimization
#Use AmberParm function to transfer the topology and
#coordinate file to the object OpenMM can use
Ambermol = AmberParm('OptC4.top', options.cfile)
# Create the OpenMM system
print('Creating OpenMM System')
if options.simupha == 'gas':
system = Ambermol.createSystem(nonbondedMethod=app.NoCutoff)
elif options.simupha == 'liquid':
system = Ambermol.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8.0*u.angstroms,
constraints=app.HBonds,)
# Create the integrator to do Langevin dynamics
# Temperature of heat bath, Friction coefficient, Time step
integrator = mm.LangevinIntegrator(300*u.kelvin, 1.0/u.picoseconds,
1.0*u.femtoseconds,)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not
# specify the platform to use the default (fastest) platform
# Create the Simulation object
if options.platf == 'ref':
platform = mm.Platform.getPlatformByName('Reference')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cpu':
platform = mm.Platform.getPlatformByName('CPU')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cuda':
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
elif options.platf == 'opencl':
platform = mm.Platform.getPlatformByName('OpenCL')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
# Set the particle positions
sim.context.setPositions(Ambermol.positions)
# Output the rst file
restrt = RestartReporter(options.rfile, 100, write_velocities=False)
sim.reporters.append(restrt)
# Minimize the energy
print('Minimizing energy ' + str(options.maxsteps) + ' steps.')
sim.minimizeEnergy(maxIterations=options.maxsteps)
# Overwrite the final file
state = sim.context.getState(getPositions=True, enforcePeriodicBox=True)
restrt.report(sim, state)
print('Calculate the RMSD')
# Perform the RMSD calcualtion, using ptraj in AmberTools
os.system("cpptraj -p OptC4.top -i OptC4_ptraj.in > OptC4_ptraj.out")
ptrajof = open('OptC4_rmsd.txt', 'r')
ln = 1
for line in ptrajof:
if ln == 3:
rmsd = float(line[12:21])
ln += 1
ptrajof.close()
print('RMSD is: ', rmsd)
return rmsd
has_openmm = False
from chemistry import unit as u
from chemistry.amber import (HAS_NETCDF, AmberParm, AmberMdcrd,
AmberAsciiRestart, NetCDFTraj, NetCDFRestart)
from chemistry.openmm.reporters import (NetCDFReporter, MdcrdReporter,
ProgressReporter, RestartReporter,
StateDataReporter,
EnergyMinimizerReporter)
import os
import utils
import unittest
get_fn = utils.get_fn
skipIf = utils.skipIf
amber_gas = AmberParm(get_fn('ash.parm7'), get_fn('ash.rst7'))
amber_solv = AmberParm(get_fn('solv.prmtop'), get_fn('solv.rst7'))
@skipIf(not has_openmm, "Cannot test without OpenMM")
class TestStateDataReporter(unittest.TestCase):
def setUp(self):
if not os.path.isdir(get_fn('writes')):
os.makedirs(get_fn('writes'))
else:
for f in os.listdir(get_fn('writes')):
os.unlink(get_fn(f, written=True))
def tearDown(self):
for f in os.listdir(get_fn('writes')):
os.unlink(get_fn(f, written=True))
#!/usr/bin/env python
from __future__ import division
from simtk.unit import *
from simtk.openmm import *
from simtk.openmm.app import *
from chemistry.amber import AmberParm
parm = AmberParm('4LYT.solv10.parm7', '4LYT.solv10.equil.rst7')
system = parm.createSystem(nonbondedCutoff=8.0*angstroms, nonbondedMethod=PME,
rigidWater=True)
integrator = VerletIntegrator(1.0e-10*picoseconds)
context = Context(system, integrator)
context.setPositions(parm.positions)
state = context.getState(getEnergy=True)
