def __init__(self, prmtopFname,
inpcrdFname): # prmtopFname, inpcrdFname ):
self.prmtop = AmberPrmtopFile(prmtopFname)
self.inpcrd = AmberInpcrdFile(inpcrdFname)
# number of atoms
self.natoms = self.prmtop.topology._numAtoms
# todo: set up ff and simulation object
self.system = self.prmtop.createSystem(
nonbondedMethod=openmmff.NoCutoff) # no cutoff
self.integrator = VerletIntegrator(0.001 * picosecond)
self.simulation = Simulation(self.prmtop.topology, self.system,
self.integrator)
# Another way of setting up potential using just pdb file ( no prmtop )
# pdb = PDBFile('coords.pdb')
# forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
# system = forcefield.createSystem(pdb.topology, nonbondedMethod=ff.NoCutoff)
# integrator = VerletIntegrator(0.001*picoseconds)
# simulation = Simulation(pdb.topology, system, integrator)
# simulation.context.setPositions(pdb.positions)
# remove units
self.localCoords = self.inpcrd.positions / angstrom
self.kJtokCal = kilocalories_per_mole / kilojoules_per_mole
def __init__(self, prmtopFname, inpcrdFname): # prmtopFname, inpcrdFname ):
# reads coords.inpcrd , coords.prmtop , min.in and data
# - fnames hard coded (todo)
super(GMINAmberPotential, self).__init__(GMIN)
# self.potentialLocal = gminpot.GMINPotential(GMIN)
GMIN.initialize()
self.prmtop = AmberPrmtopFile(prmtopFname)
self.inpcrd = AmberInpcrdFile(inpcrdFname)
# number of atoms
self.natoms = self.prmtop.topology._numAtoms
self.localCoords = self.inpcrd.positions / angstrom
def __init__(self, ff_type=None, system_file=None, **kwargs):
"""Two pathways can be used starting from FF-specific files
or OpenMM XML system. Additional kwargs are variously used
depending on the forcefield / pathway that was chosen.
supported ff_type
-----------------
amber :: give a prmtop and an inpcrd
openmm :: give an XML file for the system
supported kwargs
----------------
topology :: system-specific or not depending on FF
coordinates :: source of coordinates for initial state
"""
assert (ff_type is None) or (system_file is None)
# This dict will store the API calls
# along with atom groups and force
# parameters needed to generate all
# the given restraints
self._restraints = dict()
self._topology = None
topofile = kwargs.get("topology", None)
coordfile = kwargs.get("coordinates", None)
if ff_type is not None:
if ff_type.lower() == "amber":
prmtop = AmberPrmtopFile(topofile)
inpcrd = AmberInpcrdFile(coordfile)
self.system = prmtop.createSystem(
nonbondedMethod=NoCutoff
) #CutoffNonPeriodic - according to Ada, this would be good bc its what amber does - preliminary tests show that this hurts small/medium proteins
self._topology = Topology.from_openmm(prmtop.topology)
self._positions = inpcrd
elif system_file is not None:
self.load_xml(system_file)
if topofile:
if topofile.endswith(".pdb"):
# this line is a bit silly but Topology class
# doesn't seem to directly load PDB so keeps
# the imports clean
self._topology = Topology.from_openmm(
PDBFile(topofile).topology)
else:
# Inspect and set ff_type
# TODO ff_type as instance attribute
pass
"""
from __future__ import print_function
# OpenMM
from simtk.openmm.app import AmberPrmtopFile, AmberInpcrdFile, Simulation
from simtk.openmm.app import pdbfile as openmmpdb
from simtk.openmm import *
from simtk.unit import picosecond
import simtk.openmm.app.forcefield as openmmff
#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)
all_milestones = [me.milestones[which]]
for milestone in all_milestones:
if milestone.md:
#if not milestone.openmm.prmtop_filename:
# print "prmtop file not found for milestone %d. Skipping..." % milestone.index
# continue
if not milestone.openmm.prmtop_filename:
prmtop_path = os.path.join(me.project.rootdir, milestone.directory,
'md', 'building', 'holo.parm7')
inpcrd_path = os.path.join(me.project.rootdir, milestone.directory,
'md', 'building', 'holo.rst7')
if os.path.exists(prmtop_path) and os.path.exists(inpcrd_path):
milestone.openmm.prmtop_filename = prmtop_path
milestone.openmm.inpcrd_filename = inpcrd_path
inpcrd = AmberInpcrdFile(inpcrd_path)
milestone.box_vectors = inpcrd.boxVectors
print "box_vectors:", milestone.box_vectors
else:
print "prmtop or inpcrd file not found for milestone %d. Skipping..." % milestone.index
continue
print "launching constant energy forward stage for milestone:", which
box_vectors = milestone.box_vectors
milestone.atom_selection_1 = rec_selection
milestone.atom_selection_2 = lig_selection
fwd_rev_path = os.path.join(me.project.rootdir, milestone.directory,
'md', 'fwd_rev')
traj_base = "forward"
transition_dict_total = {}
def from_amber(cls, path):
return AmberInpcrdFile(path).boxVectors
def from_amber(cls, path):
return AmberInpcrdFile(path).positions