def test_potential(self, pdbfname ):
""" tests amber potential for pdbfname
Input
-----
pdbfname = full path to pdb file
"""
# read a conformation from pdb file
print 'reading conformation from coords.pdb'
from simtk.openmm.app import pdbfile as openmmpdb
pdb = openmmpdb.PDBFile(pdbfname)
coords = pdb.getPositions() / openmm_angstrom
coords = np.reshape(np.transpose(coords), 3*len(coords), 1)
e = self.potential.getEnergy(coords)
print 'Energy (kJ/mol) = '
print e
e, g = self.potential.getEnergyGradient(coords)
gnum = self.potential.NumericalDerivative(coords, eps=1e-6)
print 'Energy (kJ/mol) = '
print e
print 'Analytic Gradient = '
print g[1:3]
print 'Numerical Gradient = '
print gnum[1:3]
print 'Num vs Analytic Gradient ='
print np.max(np.abs(gnum-g)), np.max(np.abs(gnum))
print np.max(np.abs(gnum-g)) / np.max(np.abs(gnum))
def get_random_configuration(self):
"""a starting point for basinhopping, etc."""
from simtk.openmm.app import pdbfile as openmmpdbReader
pdb = openmmpdbReader.PDBFile('coords.pdb') # todo: coords.pdb is hardcoded
coords = pdb.getPositions() / openmm_angstrom
coords = np.reshape(np.transpose(coords), 3*len(coords), 1)
return coords
def test_potential(self, pdbfname):
""" tests amber potential for pdbfname
Input
-----
pdbfname = full path to pdb file
"""
# read a conformation from pdb file
print('reading conformation from coords.pdb')
from simtk.openmm.app import pdbfile as openmmpdb
from simtk.unit import angstrom as openmm_angstrom
pdb = openmmpdb.PDBFile(pdbfname)
coords = old_div(pdb.getPositions(), openmm_angstrom)
coords = np.reshape(np.transpose(coords), 3 * len(coords), 1)
self.potential = self.get_potential()
e = self.potential.getEnergy(coords)
print('Energy (kJ/mol) = ')
print(e)
e, g = self.potential.getEnergyGradient(coords)
gnum = self.potential.NumericalDerivative(coords, eps=1e-6)
print('Energy (kJ/mol) = ')
print(e)
print('Analytic Gradient = ')
print(g[1:3])
print('Numerical Gradient = ')
print(gnum[1:3])
print('Num vs Analytic Gradient =')
print(np.max(np.abs(gnum - g)), np.max(np.abs(gnum)))
print(old_div(np.max(np.abs(gnum - g)), np.max(np.abs(gnum))))
if __name__ == "__main__":
# create topology from prmtop file
from simtk.openmm.app import AmberPrmtopFile
prmtop = AmberPrmtopFile('../../examples/amber/coords.prmtop')
scheck = sanity_check(prmtop.topology)
# get coordinates from a pdb file
from simtk.openmm.app import pdbfile as openmmpdbReader
from simtk.unit import angstrom as openmm_angstrom
pdb = openmmpdbReader.PDBFile(
'../../examples/amber/coords.pdb') # todo: coords.pdb is hardcoded
coords = pdb.getPositions() / openmm_angstrom
coords = np.reshape(np.transpose(coords), 3 * len(coords), 1)
# test
if scheck.check_CAchirality(coords):
print '\nCA chirality test passed (all L)'
else:
print '\nCA chirality test passed (atleast one D-amino acid)'
if scheck.check_cistrans(coords):
print '\npeptide cis-trans test passed (all trans)'
else:
print '\npeptide cis-trans test failed (atleast one cis)'
from simtk.unit import kilocalories_per_mole, kilojoules_per_mole, nanometer, angstrom, picosecond
import numpy
# --- Test OpenMMAmberPotential
from pele.amber.openmm_potential import OpenMMAmberPotential
# create potential for the molecule in coords.pdb
prmtopFname = '../aladipep/coords.prmtop'
inpcrdFname = '../aladipep/coords.inpcrd'
pot = OpenMMAmberPotential(prmtopFname, inpcrdFname)
# read coordinates from pdb file
from simtk.openmm.app import pdbfile as openmmpdb
pdb = openmmpdb.PDBFile('../aladipep/coords.pdb')
coords = pdb.getPositions() / angstrom
coords = numpy.reshape(numpy.transpose(coords), 3*len(coords), 1)
# compute energy and gradients
e = pot.getEnergy(coords)
print 'Energy (kJ/mol) = '
print e
e, g = pot.getEnergyGradient(coords)
gnum = pot.NumericalDerivative(coords, eps=1e-6)
print 'Energy (kJ/mol) = '
print e
print 'Analytic Gradient = '
print g[60:65]
print 'Numerical Gradient = '
print gnum[60:65]
#from sys import stdout
# ----- OpenMM
# setup using inpcrd and prmtop
prmtop = AmberPrmtopFile('coords.prmtop')
inpcrd = AmberInpcrdFile('coords.inpcrd')
system1 = prmtop.createSystem(nonbondedMethod=openmmff.NoCutoff)
integrator1 = VerletIntegrator(0.001 * picosecond)
simulation1 = Simulation(prmtop.topology, system1, integrator1)
simulation1.context.setPositions(inpcrd.positions)
# get energy
ener1 = simulation1.context.getState(getEnergy=True).getPotentialEnergy()
# setup using pdb and built-in amber ff
pdb = openmmpdb.PDBFile('coords.pdb')
forcefield = openmmff.ForceField('amber99sb.xml', 'tip3p.xml')
system2 = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmmff.NoCutoff)
integrator2 = VerletIntegrator(0.001 * picosecond)
simulation2 = Simulation(pdb.topology, system2, integrator2)
simulation2.context.setPositions(pdb.positions)
# get energy
ener2 = simulation2.context.getState(getEnergy=True).getPotentialEnergy()
# print all energies
print("Energies (kJ/mol)")
print("inpcrd/prmtop pdb (+built-in amb99sb) ")
print("-------------------------------------------------------- ")
print(ener1, ener2)
grad = np.array(grad, dtype=float)
return float(E), grad.reshape(-1)
''' ------------------------------------------------------------------- '''
if __name__ == "__main__":
# create potential for the molecule in coords.pdb
prmtopFname = '../../examples/amber/aladipep/coords.prmtop'
inpcrdFname = '../../examples/amber/aladipep/coords.inpcrd'
pot = OpenMMAmberPotential(prmtopFname, inpcrdFname)
# read coordinates from pdb file
from simtk.openmm.app import pdbfile as openmmpdb
pdb = openmmpdb.PDBFile('../../examples/amber/aladipep/coords.pdb')
coords = pdb.getPositions() / angstrom
coords = numpy.reshape(numpy.transpose(coords), 3 * len(coords), 1)
# compute energy and gradients
e = pot.getEnergy(coords)
print 'Energy (kJ/mol) = '
print e
e, g = pot.getEnergyGradient(coords)
gnum = pot.NumericalDerivative(coords, eps=1e-6)
print 'Energy (kJ/mol) = '
print e
print 'Analytic Gradient = '