def addRDF(rdf, pdbfile, xscfile=None):
"""Add to the RDF 'rdf' the distances calculated using the coordinates
from the PDB file 'pdbfile', using the xscfile 'xscfile' to get the
dimensions of the periodic box. If 'xscfile' is None, then
no periodic boundary conditions are used."""
#first get the space in which to calculate intermolecular distances
space = Cartesian()
if xscfile:
lines = open(xscfile,"r").readlines()
words = lines[0].split()
mincoords = Vector( float(words[0]), float(words[1]), float(words[2]) )
maxcoords = Vector( float(words[3]), float(words[4]), float(words[5]) )
space = PeriodicBox(mincoords, maxcoords)
#now load all of the molecules
mols = PDB().read(pdbfile)
#create a system to hold the molecules, and add them
system = System()
system.add( MoleculeGroup("molecules", mols) )
#give the space to the system
system.add( InterCLJFF() ) # bug! need to add InterCLJFF so
# that the system has a space property. This
# is fixed in new version of Sire, but is broken
# in your version
system.setProperty("space", space)
#add the RDF - this calculates the RDF for this PDB file and adds it to 'rdf'
rdf.monitor(system)
def buildSystem(forcefields):
system = System()
for forcefield in forcefields:
system.add(forcefield)
system.setProperty("space", space)
system.setProperty("switchingFunction", HarmonicSwitchingFunction(8*angstrom, 7.5*angstrom))
system.setProperty("shiftDelta", VariantProperty(2.0))
system.setProperty("coulombPower", VariantProperty(0))
return system
salt.add(m1)
salt.add(m2)
salt.add(m3)
#salt.add(c)
#salt.add(c2)
cljff = InterCLJFF("salt-salt")
cljff.add(salt)
internalff.add(salt)
system = System()
system.add(salt)
system.add(cljff)
system.add(internalff)
system.setProperty("space", PeriodicBox(Vector(20, 20, 20)))
system.add(SpaceWrapper(Vector(0, 0, 0), salt))
t.start()
print("Initial energy = %s" % system.energy())
print("(took %d ms)" % t.elapsed())
mdmove = MolecularDynamics(
salt, VelocityVerlet(),
{"velocity generator": MaxwellBoltzmann(25 * celsius)})
mdmove = MolecularDynamics(salt, DLMRigidBody())
mdmove.setTimeStep(1 * femtosecond)
do_mc = False
def loadQMMMSystem():
"""This function is called to set up the system. It sets everything
up, then returns a System object that holds the configured system"""
print("Loading the system...")
t = QTime()
if os.path.exists(s3file.val):
print("Loading existing s3 file %s..." % s3file.val)
loadsys = Sire.Stream.load(s3file.val)
else:
print("Loading from Amber files %s / %s..." %
(topfile.val, crdfile.val))
# Add the name of the ligand to the list of solute molecules
sys_scheme = NamingScheme()
sys_scheme.addSoluteResidueName(ligand_name.val)
# Load up the system. This will automatically find the protein, solute, water, solvent
# and ion molecules and assign them to different groups
loadsys = createSystem(topfile.val, crdfile.val, sys_scheme)
ligand_mol = findMolecule(loadsys, ligand_name.val)
if ligand_mol is None:
print(
"Cannot find the ligand (%s) in the set of loaded molecules!" %
ligand_name.val)
sys.exit(-1)
# Center the system with the ligand at (0,0,0)
loadsys = centerSystem(loadsys, ligand_mol)
ligand_mol = loadsys[ligand_mol.number()][0].molecule()
if reflection_radius.val is None:
loadsys = addFlexibility(loadsys, naming_scheme=sys_scheme)
else:
loadsys = addFlexibility(loadsys,
Vector(0),
reflection_radius.val,
naming_scheme=sys_scheme)
Sire.Stream.save(loadsys, s3file.val)
ligand_mol = findMolecule(loadsys, ligand_name.val)
if ligand_mol is None:
print("Cannot find the ligand (%s) in the set of loaded molecules!" %
ligand_name.val)
sys.exit(-1)
# Now build the QM/MM system
system = System("QMMM system")
if loadsys.containsProperty("reflection center"):
reflect_center = loadsys.property("reflection center").toVector()[0]
reflect_radius = float(
str(loadsys.property("reflection sphere radius")))
system.setProperty("reflection center",
AtomCoords(CoordGroup(1, reflect_center)))
system.setProperty("reflection sphere radius",
VariantProperty(reflect_radius))
space = Cartesian()
else:
space = loadsys.property("space")
if loadsys.containsProperty("average solute translation delta"):
system.setProperty("average solute translation delta", \
loadsys.property("average solute translation delta"))
if loadsys.containsProperty("average solute rotation delta"):
system.setProperty("average solute rotation delta", \
loadsys.property("average solute rotation delta"))
# create a molecule group to hold all molecules
all_group = MoleculeGroup("all")
# create a molecule group for the ligand
ligand_group = MoleculeGroup("ligand")
ligand_group.add(ligand_mol)
all_group.add(ligand_mol)
groups = []
groups.append(ligand_group)
# pull out the groups that we want from the two systems
# create a group to hold all of the fixed molecules in the bound leg
fixed_group = MoleculeGroup("fixed_molecules")
if MGName("fixed_molecules") in loadsys.mgNames():
fixed_group.add(loadsys[MGName("fixed_molecules")])
if save_pdb.val:
# write a PDB of the fixed atoms in the bound and free legs
if not os.path.exists(outdir.val):
os.makedirs(outdir.val)
PDB().write(fixed_group, "%s/fixed.pdb" % outdir.val)
# create a group to hold all of the mobile solute molecules
mobile_solutes_group = MoleculeGroup("mobile_solutes")
if MGName("mobile_solutes") in loadsys.mgNames():
mobile_solutes_group.add(loadsys[MGName("mobile_solutes")])
mobile_solutes_group.remove(ligand_mol)
if mobile_solutes_group.nMolecules() > 0:
all_group.add(mobile_solutes_group)
groups.append(mobile_solutes_group)
# create a group to hold all of the mobile solvent molecules
mobile_solvents_group = MoleculeGroup("mobile_solvents")
if MGName("mobile_solvents") in loadsys.mgNames():
mols = loadsys[MGName("mobile_solvents")]
for molnum in mols.molNums():
solvent_mol = mols[molnum][0].molecule()
mobile_solvents_group.add(solvent_mol)
all_group.add(mobile_solvents_group)
print("The number of mobile solvent molecules is %d." %
mobile_solvents_group.nMolecules())
groups.append(mobile_solvents_group)
# create the groups to hold all of the protein molecules. We will use "extract" to
# pull out only those protein atoms that are in the mobile region
protein_intra_group = MoleculeGroup("protein_intra_group")
mobile_proteins_group = MoleculeGroup("proteins")
mobile_protein_sidechains_group = MoleculeGroup("mobile_sidechains")
mobile_protein_backbones_group = MoleculeGroup("mobile_backbones")
if MGName("protein_sidechains") in loadsys.mgNames() or \
MGName("protein_backbones") in loadsys.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = loadsys[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
protein_sidechains = MoleculeGroup()
try:
protein_backbones = loadsys[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
protein_backbones = MoleculeGroup()
try:
boundary_molecules = loadsys[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
boundary_molecules = MoleculeGroup()
for molnum in all_proteins.molNums():
protein_mol = Molecule.join(all_proteins[molnum])
if protein_mol.selectedAll():
protein_intra_group.add(protein_mol)
all_group.add(protein_mol)
mobile_protein = []
if protein_sidechains.contains(molnum):
sidechains = protein_sidechains[molnum]
for sidechain in sidechains:
mobile_protein_sidechains_group.add(sidechain)
mobile_protein += sidechains
if protein_backbones.contains(molnum):
backbones = protein_backbones[molnum]
for backbone in backbones:
mobile_protein_backbones_group.add(backbone)
mobile_protein += backbones
if len(mobile_protein) > 0:
mobile_proteins_group.add(Molecule.join(mobile_protein))
else:
# only some of the atoms have been selected. We will extract
# the mobile atoms and will then update all of the other selections
print("Extracting the mobile atoms of protein %s" %
protein_mol.molecule())
new_protein_mol = protein_mol.extract()
print("Extracted %d mobile atoms from %d total atoms..." % \
(new_protein_mol.nAtoms(), protein_mol.molecule().nAtoms()))
protein_intra_group.add(new_protein_mol)
all_group.add(new_protein_mol)
mobile_protein_view = new_protein_mol.selection()
mobile_protein_view = mobile_protein_view.selectNone()
if protein_sidechains.contains(molnum):
sidechains = protein_sidechains[molnum]
for sidechain in sidechains:
view = new_protein_mol.selection()
view = view.selectNone()
for atomid in sidechain.selection().selectedAtoms():
atom = protein_mol.atom(atomid)
resatomid = ResAtomID(atom.residue().number(),
atom.name())
view = view.select(resatomid)
mobile_protein_view = mobile_protein_view.select(
resatomid)
if view.nSelected() > 0:
mobile_protein_sidechains_group.add(
PartialMolecule(new_protein_mol, view))
if protein_backbones.contains(molnum):
backbones = protein_backbones[molnum]
for backbone in backbones:
view = new_protein_mol.selection()
view = view.selectNone()
for atomid in backbone.selection().selectedAtoms():
atom = protein_mol.atom(atomid)
resatomid = ResAtomID(atom.residue().number(),
atom.name())
view = view.select(resatomid)
mobile_protein_view = mobile_protein_view.select(
resatomid)
if view.nSelected() > 0:
mobile_protein_backbones_group.add(
PartialMolecule(new_protein_mol, view))
print("Number of moved protein sidechain residues = %s" %
mobile_protein_sidechains_group.nViews())
print("Number of moved protein backbone residues = %s" %
mobile_protein_backbones_group.nViews())
if mobile_protein_view.nSelected() > 0:
mobile_proteins_group.add(
PartialMolecule(new_protein_mol, mobile_protein_view))
groups.append(mobile_protein_backbones_group)
groups.append(mobile_protein_sidechains_group)
groups.append(all_group)
# finished added in all of the proteins
for group in groups:
if group.nMolecules() > 0:
print("Adding group %s" % group.name())
system.add(group)
# now add in the forcefields for the system...
print("Creating the forcefields for the QM/MM system...")
# first, group together the molecules grouped above into convenient
# groups for the forcefields
# group holding just the ligand
ligand_mols = ligand_group.molecules()
# group holding all of the mobile atoms
mobile_mols = mobile_solvents_group.molecules()
mobile_mols.add(mobile_solutes_group.molecules())
mobile_mols.add(protein_intra_group.molecules())
# group holding all of the mobile atoms in the bound leg, excluding the
# buffer atoms that are fixed, but bonded to mobile atoms
mobile_buffered_mols = mobile_solvents_group.molecules()
mobile_buffered_mols.add(mobile_solutes_group.molecules())
mobile_buffered_mols.add(mobile_proteins_group.molecules())
# group holding all of the protein molecules that need intramolecular terms calculated
protein_intra_mols = protein_intra_group.molecules()
# group holding all of the solute molecules that nede intramolecular terms calculated
solute_intra_mols = mobile_solutes_group.molecules()
forcefields = []
###
### INTRA-ENERGY OF THE LIGAND AND CLUSTER
###
# intramolecular energy of the ligand
ligand_intraclj = IntraCLJFF("ligand:intraclj")
ligand_intraclj = setCLJProperties(ligand_intraclj, space)
ligand_intraclj.add(ligand_mols)
ligand_intraff = InternalFF("ligand:intra")
ligand_intraff.add(ligand_mols)
forcefields.append(ligand_intraclj)
forcefields.append(ligand_intraff)
ligand_mm_nrg = ligand_intraclj.components().total(
) + ligand_intraff.components().total()
###
### FORCEFIELDS INVOLVING THE LIGAND/CLUSTER AND OTHER ATOMS
###
# forcefield holding the energy between the ligand and the mobile atoms in the
# bound leg
ligand_mobile = InterGroupCLJFF("system:ligand-mobile")
ligand_mobile = setCLJProperties(ligand_mobile, space)
ligand_mobile.add(ligand_mols, MGIdx(0))
ligand_mobile.add(mobile_mols, MGIdx(1))
qm_ligand = QMMMFF("system:ligand-QM")
qm_ligand.add(ligand_mols, MGIdx(0))
qm_ligand = setQMProperties(qm_ligand, space)
zero_energy = 0
if not intermolecular_only.val:
if qm_zero_energy.val is None:
# calculate the delta value for the system - this is the difference between
# the MM and QM intramolecular energy of the ligand
t.start()
print("\nComparing the MM and QM energies of the ligand...")
mm_intra = ligand_intraclj.energy().value(
) + ligand_intraff.energy().value()
print("MM energy = %s kcal mol-1 (took %s ms)" %
(mm_intra, t.elapsed()))
t.start()
zero_sys = System()
zero_sys.add(qm_ligand)
qm_intra = zero_sys.energy().value()
print("QM energy = %s kcal mol-1 (took %s ms)" %
(qm_intra, t.elapsed()))
print("\nSetting the QM zero energy to %s kcal mol-1" %
(qm_intra - mm_intra))
qm_ligand.setZeroEnergy((qm_intra - mm_intra) * kcal_per_mol)
zero_energy = qm_intra - mm_intra
else:
print("\nManually setting the QM zero energy to %s" %
qm_zero_energy.val)
qm_ligand.setZeroEnergy(qm_zero_energy.val)
zero_energy = qm_zero_energy.val
qm_ligand.add(mobile_mols, MGIdx(1))
ligand_mm_nrg += ligand_mobile.components().total()
ligand_qm_nrg = qm_ligand.components().total() + ligand_mobile.components(
).lj()
if intermolecular_only.val:
# the QM model still uses the MM intramolecular energy of the ligand
ligand_qm_nrg += ligand_intraclj.components().total(
) + ligand_intraff.components().total()
forcefields.append(ligand_mobile)
forcefields.append(qm_ligand)
if fixed_group.nMolecules() > 0:
# there are fixed molecules
# Whether or not to disable the grid and calculate all energies atomisticly
if disable_grid:
# we need to renumber all of the fixed molecules so that they don't clash
# with the mobile molecules
print("Renumbering fixed molecules...")
fixed_group = renumberMolecules(fixed_group)
# forcefield holding the energy between the ligand and the fixed atoms in the bound leg
if disable_grid:
ligand_fixed = InterGroupCLJFF("system:ligand-fixed")
ligand_fixed = setCLJProperties(ligand_fixed, space)
ligand_fixed = setFakeGridProperties(ligand_fixed, space)
ligand_fixed.add(ligand_mols, MGIdx(0))
ligand_fixed.add(fixed_group, MGIdx(1))
qm_ligand.add(fixed_group, MGIdx(1))
ligand_mm_nrg += ligand_fixed.components().total()
ligand_qm_nrg += ligand_fixed.components().lj()
forcefields.append(ligand_fixed)
else:
ligand_fixed = GridFF2("system:ligand-fixed")
ligand_fixed = setCLJProperties(ligand_fixed, space)
ligand_fixed = setGridProperties(ligand_fixed)
ligand_fixed.add(ligand_mols, MGIdx(0))
ligand_fixed.addFixedAtoms(fixed_group)
qm_ligand.addFixedAtoms(fixed_group)
ligand_mm_nrg += ligand_fixed.components().total()
ligand_qm_nrg += ligand_fixed.components().lj()
forcefields.append(ligand_fixed)
###
### FORCEFIELDS NOT INVOLVING THE LIGAND
###
# forcefield holding the intermolecular energy between all molecules
mobile_mobile = InterCLJFF("mobile-mobile")
mobile_mobile = setCLJProperties(mobile_mobile, space)
mobile_mobile.add(mobile_mols)
other_nrg = mobile_mobile.components().total()
forcefields.append(mobile_mobile)
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
mobile_fixed = InterGroupCLJFF("mobile-fixed")
mobile_fixed = setCLJProperties(mobile_fixed)
mobile_fixed = setFakeGridProperties(mobile_fixed, space)
mobile_fixed.add(mobile_buffered_mols, MGIdx(0))
mobile_fixed.add(fixed_group, MGIdx(1))
other_nrg += mobile_fixed.components().total()
forcefields.append(mobile_fixed)
else:
mobile_fixed = GridFF2("mobile-fixed")
mobile_fixed = setCLJProperties(mobile_fixed, space)
mobile_fixed = setGridProperties(mobile_fixed)
# we use mobile_buffered_group as this group misses out atoms that are bonded
# to fixed atoms (thus preventing large energies caused by incorrect non-bonded calculations)
mobile_fixed.add(mobile_buffered_mols, MGIdx(0))
mobile_fixed.addFixedAtoms(fixed_group)
other_nrg += mobile_fixed.components().total()
forcefields.append(mobile_fixed)
# intramolecular energy of the protein
if protein_intra_mols.nMolecules() > 0:
protein_intraclj = IntraCLJFF("protein_intraclj")
protein_intraclj = setCLJProperties(protein_intraclj, space)
protein_intraff = InternalFF("protein_intra")
for molnum in protein_intra_mols.molNums():
protein_mol = Molecule.join(protein_intra_mols[molnum])
protein_intraclj.add(protein_mol)
protein_intraff.add(protein_mol)
other_nrg += protein_intraclj.components().total()
other_nrg += protein_intraff.components().total()
forcefields.append(protein_intraclj)
forcefields.append(protein_intraff)
# intramolecular energy of any other solutes
if solute_intra_mols.nMolecules() > 0:
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj = setCLJProperties(solute_intraclj, space)
solute_intraff = InternalFF("solute_intra")
for molnum in solute_intra_mols.molNums():
solute_mol = Molecule.join(solute_intra_mols[molnum])
solute_intraclj.add(solute_mol)
solute_intraff.add(solute_mol)
other_nrg += solute_intraclj.components().total()
other_nrg += solute_intraff.components().total()
forcefields.append(solute_intraclj)
forcefields.append(solute_intraff)
###
### NOW ADD THE FORCEFIELDS TO THE SYSTEM
###
###
### SETTING THE FORCEFIELD EXPRESSIONS
###
lam = Symbol("lambda")
e_slow = ((1 - lam) * ligand_qm_nrg) + (lam * ligand_mm_nrg) + other_nrg
e_fast = ligand_mm_nrg + other_nrg
de_by_dlam = ligand_mm_nrg - ligand_qm_nrg
for forcefield in forcefields:
system.add(forcefield)
system.setConstant(lam, 0.0)
system.setComponent(Symbol("E_{fast}"), e_fast)
system.setComponent(Symbol("E_{slow}"), e_slow)
system.setComponent(Symbol("dE/dlam"), de_by_dlam)
system.setComponent(system.totalComponent(), e_slow)
system.setProperty("space", space)
if space.isPeriodic():
# ensure that all molecules are wrapped into the space with the ligand at the center
print("Adding in a space wrapper constraint %s, %s" %
(space, ligand_mol.evaluate().center()))
system.add(SpaceWrapper(ligand_mol.evaluate().center(), all_group))
system.applyConstraints()
print("\nHere are the values of all of the initial energy components...")
t.start()
printEnergies(system.energies())
print("(these took %d ms to evaluate)\n" % t.elapsed())
# Create a monitor to monitor the free energy average
system.add("dG/dlam",
MonitorComponent(Symbol("dE/dlam"), AverageAndStddev()))
if intermolecular_only.val:
print(
"\n\n## This simulation uses QM to model *only* the intermolecular energy between"
)
print(
"## the QM and MM atoms. The intramolecular energy of the QM atoms is still"
)
print("## modelled using MM.\n")
else:
print(
"\n\n## This simulation uses QM to model both the intermolecular and intramolecular"
)
print(
"## energies of the QM atoms. Because the this, we have to adjust the 'zero' point"
)
print(
"## of the QM potential. You need to add the value %s kcal mol-1 back onto the"
% zero_energy)
print("## QM->MM free energy calculated using this program.\n")
return system
system = System()
for forcefield in forcefields:
forcefield.add(protein)
system.add(forcefield)
def printEnergies(nrgs):
keys = list(nrgs.keys())
keys.sort()
for key in keys:
print("%25s : %12.8f" % (key, nrgs[key]))
system.setProperty("switchingFunction",
HarmonicSwitchingFunction(10 * angstrom, 9.5 * angstrom))
printEnergies(system.energies())
print("\nEnergy with respect to cutoff length\n")
print(" Distance Group Shifted ReactionField ")
for i in range(10, 501, 5):
x = i * 0.1
switchfunc = HarmonicSwitchingFunction(x * angstrom, (x - 0.5) * angstrom)
system.setProperty("switchingFunction", switchfunc)
print(
"%12.8f %12.8f %12.8f %12.8f" %
(x, system.energy(group_coul).value(),
from Sire.System import *
from Sire.IO import *
from Sire.FF import *
from Sire.Maths import *
from Sire.Mol import *
from Sire.Vol import *
mols = PDB().read("test/io/water.pdb")
solvent = MoleculeGroup("solvent", mols)
system = System()
system.add(solvent)
system.setProperty("space", Cartesian())
points = [
Vector(10, 10, 10),
solvent.moleculeAt(0).atom(AtomName("O00")),
Vector(0, 0, 0),
Vector(5, 5, 5)
]
print(solvent.moleculeAt(0).molecule().number())
idassigner = IDAssigner(points, solvent)
points = idassigner.points()
idassigner.update(system)
mols = idassigner.identifiedMolecules()
def loadQMMMSystem():
"""This function is called to set up the system. It sets everything
up, then returns a System object that holds the configured system"""
print("Loading the system...")
t = QTime()
if os.path.exists(s3file.val):
print("Loading existing s3 file %s..." % s3file.val)
loadsys = Sire.Stream.load(s3file.val)
else:
print("Loading from Amber files %s / %s..." % (topfile.val, crdfile.val))
# Add the name of the ligand to the list of solute molecules
sys_scheme = NamingScheme()
sys_scheme.addSoluteResidueName(ligand_name.val)
# Load up the system. This will automatically find the protein, solute, water, solvent
# and ion molecules and assign them to different groups
loadsys = createSystem(topfile.val, crdfile.val, sys_scheme)
ligand_mol = findMolecule(loadsys, ligand_name.val)
if ligand_mol is None:
print("Cannot find the ligand (%s) in the set of loaded molecules!" % ligand_name.val)
sys.exit(-1)
# Center the system with the ligand at (0,0,0)
loadsys = centerSystem(loadsys, ligand_mol)
ligand_mol = loadsys[ligand_mol.number()].molecule()
if reflection_radius.val is None:
loadsys = addFlexibility(loadsys, naming_scheme=sys_scheme )
else:
loadsys = addFlexibility(loadsys, Vector(0), reflection_radius.val, naming_scheme=sys_scheme)
Sire.Stream.save(loadsys, s3file.val)
ligand_mol = findMolecule(loadsys, ligand_name.val)
if ligand_mol is None:
print("Cannot find the ligand (%s) in the set of loaded molecules!" % ligand_name.val)
sys.exit(-1)
# Now build the QM/MM system
system = System("QMMM system")
if loadsys.containsProperty("reflection center"):
reflect_center = loadsys.property("reflection center").toVector()[0]
reflect_radius = float(str(loadsys.property("reflection sphere radius")))
system.setProperty("reflection center", AtomCoords(CoordGroup(1,reflect_center)))
system.setProperty("reflection sphere radius", VariantProperty(reflect_radius))
space = Cartesian()
else:
space = loadsys.property("space")
if loadsys.containsProperty("average solute translation delta"):
system.setProperty("average solute translation delta", \
loadsys.property("average solute translation delta"))
if loadsys.containsProperty("average solute rotation delta"):
system.setProperty("average solute rotation delta", \
loadsys.property("average solute rotation delta"))
# create a molecule group to hold all molecules
all_group = MoleculeGroup("all")
# create a molecule group for the ligand
ligand_group = MoleculeGroup("ligand")
ligand_group.add(ligand_mol)
all_group.add(ligand_mol)
groups = []
groups.append(ligand_group)
# pull out the groups that we want from the two systems
# create a group to hold all of the fixed molecules in the bound leg
fixed_group = MoleculeGroup("fixed_molecules")
if MGName("fixed_molecules") in loadsys.mgNames():
fixed_group.add( loadsys[ MGName("fixed_molecules") ] )
if save_pdb.val:
# write a PDB of the fixed atoms in the bound and free legs
if not os.path.exists(outdir.val):
os.makedirs(outdir.val)
PDB().write(fixed_group, "%s/fixed.pdb" % outdir.val)
# create a group to hold all of the mobile solute molecules
mobile_solutes_group = MoleculeGroup("mobile_solutes")
if MGName("mobile_solutes") in loadsys.mgNames():
mobile_solutes_group.add( loadsys[MGName("mobile_solutes")] )
mobile_solutes_group.remove(ligand_mol)
if mobile_solutes_group.nMolecules() > 0:
all_group.add(mobile_solutes_group)
groups.append(mobile_solutes_group)
# create a group to hold all of the mobile solvent molecules
mobile_solvents_group = MoleculeGroup("mobile_solvents")
if MGName("mobile_solvents") in loadsys.mgNames():
mols = loadsys[MGName("mobile_solvents")]
for molnum in mols.molNums():
solvent_mol = mols[molnum].molecule()
mobile_solvents_group.add(solvent_mol)
all_group.add(mobile_solvents_group)
print("The number of mobile solvent molecules is %d." % mobile_solvents_group.nMolecules())
groups.append(mobile_solvents_group)
# create the groups to hold all of the protein molecules. We will use "extract" to
# pull out only those protein atoms that are in the mobile region
protein_intra_group = MoleculeGroup("protein_intra_group")
mobile_proteins_group = MoleculeGroup("proteins")
mobile_protein_sidechains_group = MoleculeGroup("mobile_sidechains")
mobile_protein_backbones_group = MoleculeGroup("mobile_backbones")
if MGName("protein_sidechains") in loadsys.mgNames() or \
MGName("protein_backbones") in loadsys.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = loadsys[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
protein_sidechains = MoleculeGroup()
try:
protein_backbones = loadsys[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
protein_backbones = MoleculeGroup()
try:
boundary_molecules = loadsys[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
boundary_molecules = MoleculeGroup()
for molnum in all_proteins.molNums():
protein_mol = all_proteins[molnum].join()
if protein_mol.selectedAll():
protein_intra_group.add(protein_mol)
all_group.add(protein_mol)
mobile_protein = None
try:
mobile_protein = protein_sidechains[molnum]
mobile_protein_sidechains_group.add( mobile_protein )
except:
pass
try:
if mobile_protein is None:
mobile_protein = protein_backbones[molnum]
mobile_protein_backbones_group.add( mobile_protein )
else:
mobile_protein.add( protein_backbones[molnum].selection() )
mobile_protein_backbones_group.add( protein_backbones[molnum] )
except:
pass
if not (mobile_protein is None):
mobile_proteins_group.add( mobile_protein.join() )
else:
# only some of the atoms have been selected. We will extract
# the mobile atoms and will then update all of the other selections
print("Extracting the mobile atoms of protein %s" % protein_mol)
new_protein_mol = protein_mol.extract()
print("Extracted %d mobile atoms from %d total atoms..." % \
(new_protein_mol.nAtoms(), protein_mol.molecule().nAtoms()))
protein_intra_group.add(new_protein_mol)
all_group.add( new_protein_mol )
mobile_protein_view = new_protein_mol.selection()
mobile_protein_view = mobile_protein_view.selectNone()
try:
sidechains = protein_sidechains[molnum]
for i in range(0,sidechains.nViews()):
view = new_protein_mol.selection()
view = view.selectNone()
for atomid in sidechains.viewAt(i).selectedAtoms():
atom = protein_mol.atom(atomid)
resatomid = ResAtomID( atom.residue().number(), atom.name() )
view = view.select( resatomid )
mobile_protein_view = mobile_protein_view.select( resatomid )
if view.nSelected() > 0:
mobile_protein_sidechains_group.add( PartialMolecule(new_protein_mol, view) )
except:
pass
try:
backbones = protein_backbones[molnum]
for i in range(0,backbones.nViews()):
view = new_protein_mol.selection()
view = view.selectNone()
for atomid in backbones.viewAt(i).selectedAtoms():
atom = protein_mol.atom(atomid)
resatomid = ResAtomID( atom.residue().number(), atom.name() )
view = view.select( resatomid )
mobile_protein_view = mobile_protein_view.select( resatomid )
if view.nSelected() > 0:
mobile_protein_backbones_group.add( PartialMolecule(new_protein_mol, view) )
except:
pass
if mobile_protein_view.nSelected() > 0:
mobile_proteins_group.add( PartialMolecule(new_protein_mol, mobile_protein_view) )
groups.append(mobile_protein_backbones_group)
groups.append(mobile_protein_sidechains_group)
groups.append(all_group)
# finished added in all of the proteins
for group in groups:
if group.nMolecules() > 0:
print("Adding group %s" % group.name())
system.add(group)
# now add in the forcefields for the system...
print("Creating the forcefields for the QM/MM system...")
# first, group together the molecules grouped above into convenient
# groups for the forcefields
# group holding just the ligand
ligand_mols = ligand_group.molecules()
# group holding all of the mobile atoms
mobile_mols = mobile_solvents_group.molecules()
mobile_mols.add( mobile_solutes_group.molecules() )
mobile_mols.add( protein_intra_group.molecules() )
# group holding all of the mobile atoms in the bound leg, excluding the
# buffer atoms that are fixed, but bonded to mobile atoms
mobile_buffered_mols = mobile_solvents_group.molecules()
mobile_buffered_mols.add( mobile_solutes_group.molecules() )
mobile_buffered_mols.add( mobile_proteins_group.molecules() )
# group holding all of the protein molecules that need intramolecular terms calculated
protein_intra_mols = protein_intra_group.molecules()
# group holding all of the solute molecules that nede intramolecular terms calculated
solute_intra_mols = mobile_solutes_group.molecules()
forcefields = []
###
### INTRA-ENERGY OF THE LIGAND AND CLUSTER
###
# intramolecular energy of the ligand
ligand_intraclj = IntraCLJFF("ligand:intraclj")
ligand_intraclj = setCLJProperties(ligand_intraclj, space)
ligand_intraclj.add(ligand_mols)
ligand_intraff = InternalFF("ligand:intra")
ligand_intraff.add(ligand_mols)
forcefields.append(ligand_intraclj)
forcefields.append(ligand_intraff)
ligand_mm_nrg = ligand_intraclj.components().total() + ligand_intraff.components().total()
###
### FORCEFIELDS INVOLVING THE LIGAND/CLUSTER AND OTHER ATOMS
###
# forcefield holding the energy between the ligand and the mobile atoms in the
# bound leg
ligand_mobile = InterGroupCLJFF("system:ligand-mobile")
ligand_mobile = setCLJProperties(ligand_mobile, space)
ligand_mobile.add(ligand_mols, MGIdx(0))
ligand_mobile.add(mobile_mols, MGIdx(1))
qm_ligand = QMMMFF("system:ligand-QM")
qm_ligand = setQMProperties(qm_ligand, space)
qm_ligand.add(ligand_mols, MGIdx(0))
zero_energy = 0
if not intermolecular_only.val:
if qm_zero_energy.val is None:
# calculate the delta value for the system - this is the difference between
# the MM and QM intramolecular energy of the ligand
t.start()
print("\nComparing the MM and QM energies of the ligand...")
mm_intra = ligand_intraclj.energy().value() + ligand_intraff.energy().value()
print("MM energy = %s kcal mol-1 (took %s ms)" % (mm_intra, t.elapsed()))
t.start()
qm_intra = qm_ligand.energy().value()
print("QM energy = %s kcal mol-1 (took %s ms)" % (qm_intra, t.elapsed()))
print("\nSetting the QM zero energy to %s kcal mol-1" % (qm_intra - mm_intra))
qm_ligand.setZeroEnergy( (qm_intra-mm_intra) * kcal_per_mol )
zero_energy = qm_intra - mm_intra
else:
print("\nManually setting the QM zero energy to %s" % qm_zero_energy.val)
qm_ligand.setZeroEnergy( qm_zero_energy.val )
zero_energy = qm_zero_energy.val
qm_ligand.add(mobile_mols, MGIdx(1))
ligand_mm_nrg += ligand_mobile.components().total()
ligand_qm_nrg = qm_ligand.components().total() + ligand_mobile.components().lj()
if intermolecular_only.val:
# the QM model still uses the MM intramolecular energy of the ligand
ligand_qm_nrg += ligand_intraclj.components().total() + ligand_intraff.components().total()
forcefields.append(ligand_mobile)
forcefields.append(qm_ligand)
if fixed_group.nMolecules() > 0:
# there are fixed molecules
# Whether or not to disable the grid and calculate all energies atomisticly
if disable_grid:
# we need to renumber all of the fixed molecules so that they don't clash
# with the mobile molecules
print("Renumbering fixed molecules...")
fixed_group = renumberMolecules(fixed_group)
# forcefield holding the energy between the ligand and the fixed atoms in the bound leg
if disable_grid:
ligand_fixed = InterGroupCLJFF("system:ligand-fixed")
ligand_fixed = setCLJProperties(ligand_fixed, space)
ligand_fixed = setFakeGridProperties(ligand_fixed, space)
ligand_fixed.add(ligand_mols, MGIdx(0))
ligand_fixed.add(fixed_group, MGIdx(1))
qm_ligand.add(fixed_group, MGIdx(1))
ligand_mm_nrg += ligand_fixed.components().total()
ligand_qm_nrg += ligand_fixed.components().lj()
forcefields.append(ligand_fixed)
else:
ligand_fixed = GridFF("system:ligand-fixed")
ligand_fixed = setCLJProperties(ligand_fixed, space)
ligand_fixed = setGridProperties(ligand_fixed)
ligand_fixed.add(ligand_mols, MGIdx(0))
ligand_fixed.addFixedAtoms( fixed_group )
qm_ligand.addFixedAtoms( fixed_group )
ligand_mm_nrg += ligand_fixed.components().total()
ligand_qm_nrg += ligand_fixed.components().lj()
forcefields.append(ligand_fixed)
###
### FORCEFIELDS NOT INVOLVING THE LIGAND
###
# forcefield holding the intermolecular energy between all molecules
mobile_mobile = InterCLJFF("mobile-mobile")
mobile_mobile = setCLJProperties(mobile_mobile, space)
mobile_mobile.add(mobile_mols)
other_nrg = mobile_mobile.components().total()
forcefields.append(mobile_mobile)
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
mobile_fixed = InterGroupCLJFF("mobile-fixed")
mobile_fixed = setCLJProperties(mobile_fixed)
mobile_fixed = setFakeGridProperties(mobile_fixed, space)
mobile_fixed.add(mobile_buffered_mols, MGIdx(0))
mobile_fixed.add(fixed_group, MGIdx(1))
other_nrg += mobile_fixed.components().total()
forcefields.append(mobile_fixed)
else:
mobile_fixed = GridFF("mobile-fixed")
mobile_fixed = setCLJProperties(mobile_fixed, space)
mobile_fixed = setGridProperties(mobile_fixed)
# we use mobile_buffered_group as this group misses out atoms that are bonded
# to fixed atoms (thus preventing large energies caused by incorrect non-bonded calculations)
mobile_fixed.add(mobile_buffered_mols, MGIdx(0))
mobile_fixed.addFixedAtoms(fixed_group)
other_nrg += mobile_fixed.components().total()
forcefields.append(mobile_fixed)
# intramolecular energy of the protein
if protein_intra_mols.nMolecules() > 0:
protein_intraclj = IntraCLJFF("protein_intraclj")
protein_intraclj = setCLJProperties(protein_intraclj, space)
protein_intraff = InternalFF("protein_intra")
for molnum in protein_intra_mols.molNums():
protein_mol = protein_intra_mols[molnum].join()
protein_intraclj.add(protein_mol)
protein_intraff.add(protein_mol)
other_nrg += protein_intraclj.components().total()
other_nrg += protein_intraff.components().total()
forcefields.append(protein_intraclj)
forcefields.append(protein_intraff)
# intramolecular energy of any other solutes
if solute_intra_mols.nMolecules() > 0:
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj = setCLJProperties(solute_intraclj, space)
solute_intraff = InternalFF("solute_intra")
for molnum in solute_intra_mols.molNums():
solute_mol = solute_intra_mols[molnum].join()
solute_intraclj.add(solute_mol)
solute_intraff.add(solute_mol)
other_nrg += solute_intraclj.components().total()
other_nrg += solute_intraff.components().total()
forcefields.append(solute_intraclj)
forcefields.append(solute_intraff)
###
### NOW ADD THE FORCEFIELDS TO THE SYSTEM
###
###
### SETTING THE FORCEFIELD EXPRESSIONS
###
lam = Symbol("lambda")
e_slow = ((1-lam) * ligand_qm_nrg) + (lam * ligand_mm_nrg) + other_nrg
e_fast = ligand_mm_nrg + other_nrg
de_by_dlam = ligand_mm_nrg - ligand_qm_nrg
for forcefield in forcefields:
system.add(forcefield)
system.setConstant(lam, 0.0)
system.setComponent(Symbol("E_{fast}"), e_fast)
system.setComponent(Symbol("E_{slow}"), e_slow)
system.setComponent(Symbol("dE/dlam"), de_by_dlam)
system.setComponent( system.totalComponent(), e_slow )
system.setProperty("space", space)
if space.isPeriodic():
# ensure that all molecules are wrapped into the space with the ligand at the center
print("Adding in a space wrapper constraint %s, %s" % (space, ligand_mol.evaluate().center()))
system.add( SpaceWrapper( ligand_mol.evaluate().center(), all_group ) )
system.applyConstraints()
print("\nHere are the values of all of the initial energy components...")
t.start()
printEnergies(system.energies())
print("(these took %d ms to evaluate)\n" % t.elapsed())
# Create a monitor to monitor the free energy average
system.add( "dG/dlam", MonitorComponent(Symbol("dE/dlam"), AverageAndStddev()) )
if intermolecular_only.val:
print("\n\n## This simulation uses QM to model *only* the intermolecular energy between")
print("## the QM and MM atoms. The intramolecular energy of the QM atoms is still")
print("## modelled using MM.\n")
else:
print("\n\n## This simulation uses QM to model both the intermolecular and intramolecular")
print("## energies of the QM atoms. Because the this, we have to adjust the 'zero' point")
print("## of the QM potential. You need to add the value %s kcal mol-1 back onto the" % zero_energy)
print("## QM->MM free energy calculated using this program.\n")
return system
waters.setName("water")
# Create a system to hold the system to be simulated
system = System()
# Add the waters to the system
system.add(waters)
# create a forcefield to calculate the intermolecular
# Coulomb and Lennard-Jones energies of the waters (CLJ)
cljff = InterFF("cljff")
# Use a shift-electrostatics with a 10 angstrom cutoff
cljff.setCLJFunction( CLJShiftFunction(10*angstrom) )
# Add the waters and set the cutoff to 10 angstroms
cljff.add(waters)
# Add the forcefield to the system
system.add(cljff)
# Tell the system about the periodic box
system.setProperty("space", space)
system.add( SpaceWrapper(Vector(0), waters) )
system.applyConstraints()
# Save a binary representation of the system
# to the file "waterbox.s3"
import Sire.Stream
Sire.Stream.save( system, "waterbox.s3" )
solvent.update(mol)
system = System()
system.add(solute)
system.add(solvent)
solvent_cljff = InterCLJFF("solvent_cljff")
solvent_cljff.add(solvent)
solute_solvent_cljff = InterGroupCLJFF("solute_solvent_cljff")
solute_solvent_cljff.add( solute, MGIdx(0) )
solute_solvent_cljff.add( solvent, MGIdx(1) )
system.add(solvent_cljff)
system.add(solute_solvent_cljff)
system.setProperty("space", PeriodicBox( Vector(-18.3854,-18.66855,-18.4445),
Vector( 18.3854, 18.66855, 18.4445) ) )
print("Equilibrating the system...")
solvent_move = RigidBodyMC( PrefSampler(solute.moleculeAt(0), solvent, 200*angstrom2) )
solvent_move.setMaximumTranslation( 0.2 * angstrom )
solvent_move.setMaximumRotation( 5 * degrees )
solute_move = RigidBodyMC( solute )
solute_move.setMaximumTranslation( 0.2 * angstrom )
solute_move.setMaximumRotation( 5 * degrees )
moves = WeightedMoves()
moves.add( solvent_move, 100 )
moves.add( solute_move, 1 )
# The protein-solvent energy
protein_solventff = InterGroupCLJFF("protein:solvent")
protein_solventff.add(protein, MGIdx(0))
protein_solventff.add(solvent, MGIdx(1))
# Here is the list of all forcefields
forcefields = [ solute_intraff, solute_intraclj,
solventff, solute_solventff,
protein_intraff, protein_intraclj,
solute_proteinff, protein_solventff ]
# Add these forcefields to the system
for forcefield in forcefields:
system.add(forcefield)
system.setProperty( "space", space )
system.setProperty( "switchingFunction",
HarmonicSwitchingFunction(coulomb_cutoff, coulomb_feather,
lj_cutoff, lj_feather) )
system.setProperty( "combiningRules", VariantProperty(combining_rules) )
total_nrg = solute_intraclj.components().total() + solute_intraff.components().total() +\
solventff.components().total() + solute_solventff.components().total() +\
protein_intraclj.components().total() + protein_intraff.components().total() + \
solute_proteinff.components().total() + protein_solventff.components().total()
e_total = system.totalComponent()
system.setComponent( e_total, total_nrg )
# Add a space wrapper that wraps all molecules into the box centered at (0,0,0)
#system.add( SpaceWrapper(Vector(0,0,0), all) )
system = System()
for forcefield in forcefields:
forcefield.add(waters)
system.add(forcefield)
def printEnergies(nrgs):
keys = list(nrgs.keys())
keys.sort()
for key in keys:
print("%25s : %12.8f" % (key, nrgs[key]))
system.setProperty("space", space)
system.setProperty("switchingFunction", switchfunc)
printEnergies(system.energies())
print("\nEnergy with respect to cutoff length\n")
print(" Distance Group Shifted ReactionField Atomistic")
for i in range(10, 200, 5):
x = i * 0.1
switchfunc = HarmonicSwitchingFunction(x * angstrom, (x - 0.5) * angstrom)
system.setProperty("switchingFunction", switchfunc)
print(
"%12.8f %12.8f %12.8f %12.8f %12.8f" %
def makeSim(system, ligand_mol, watersys):
"""Create simulation systems with and without the ligand and return those systems together
with the moves"""
stage1 = System("with_ligand")
stage2 = System("without_ligand")
if system.containsProperty("reflection center"):
reflection_center = system.property("reflection center").toVector()[0]
reflection_radius = float(str(system.property("reflection sphere radius")))
stage1.setProperty("reflection center", AtomCoords(CoordGroup(1,reflection_center)))
stage1.setProperty("reflection sphere radius", VariantProperty(reflection_radius))
stage2.setProperty("reflection center", AtomCoords(CoordGroup(1,reflection_center)))
stage2.setProperty("reflection sphere radius", VariantProperty(reflection_radius))
# create a molecule group for fixed atoms (everything except the mobile water)
fixed_group = MoleculeGroup("fixed")
if MGName("fixed_molecules") in system.mgNames():
fixed_group.add( system[ MGName("fixed_molecules") ] )
if MGName("mobile_solutes") in system.mgNames():
fixed_group.add( system[MGName("mobile_solutes")] )
if MGName("protein_sidechains") in system.mgNames() or \
MGName("protein_backbones") in system.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = system[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
pass
try:
protein_backbones = system[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
pass
try:
boundary_molecules = system[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
pass
for molnum in all_proteins.molNums():
protein_mol = all_proteins[molnum].join()
fixed_group.add(protein_mol)
stage1_fixed_group = MoleculeGroup(fixed_group)
stage2_fixed_group = MoleculeGroup(fixed_group)
stage1_fixed_group.add(ligand_mol)
stage2_fixed_group.remove(ligand_mol)
mobile_group = MoleculeGroup("mobile_group")
if MGName("mobile_solvents") in system.mgNames():
mobile_group.add( system[MGName("mobile_solvents")] )
stage1_mobile_group = MoleculeGroup(mobile_group)
stage2_mobile_group = MoleculeGroup(mobile_group)
# now find water molecules from the water system that can be substituted for the ligand
watermols = findOverlappingWaters(ligand_mol, watersys)
stage2_mobile_group.add(watermols)
print("The number of stage 1 fixed non-solvent molecules is %d." % stage1_fixed_group.nMolecules())
print("The number of stage 1 mobile solvent molecules is %d." % stage1_mobile_group.nMolecules())
print("The number of stage 2 fixed non-solvent molecules is %d." % stage2_fixed_group.nMolecules())
print("The number of stage 2 mobile solvent molecules is %d." % stage2_mobile_group.nMolecules())
# write a PDB of all of the fixed molecules
PDB().write(stage1_mobile_group, "stage1_mobile_atoms.pdb")
PDB().write(stage2_mobile_group, "stage2_mobile_atoms.pdb")
PDB().write(stage1_fixed_group, "stage1_fixed_atoms.pdb")
PDB().write(stage2_fixed_group, "stage2_fixed_atoms.pdb")
# create the forcefields
if use_fast_ff.val:
stage1_ff = InterFF("ff")
stage2_ff = InterFF("ff")
stage1_ff.setCLJFunction( CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val) )
stage2_ff.setCLJFunction( CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val) )
if disable_grid.val:
stage1_ff.disableGrid()
stage2_ff.disableGrid()
else:
stage1_ff.enableGrid()
stage1_ff.setGridSpacing(grid_spacing.val)
stage1_ff.setGridBuffer(grid_buffer.val)
stage2_ff.enableGrid()
stage2_ff.setGridSpacing(grid_spacing.val)
stage2_ff.setGridBuffer(grid_buffer.val)
stage1_ff.add(stage1_mobile_group)
stage1_ff.setFixedAtoms(stage1_fixed_group.molecules())
stage2_ff.add(stage2_mobile_group)
stage2_ff.setFixedAtoms(stage2_fixed_group.molecules())
stage1.add(stage1_ff)
stage1.setComponent(stage1.totalComponent(), stage1_ff.components().total())
stage2.add(stage1_ff)
stage2.setComponent(stage2.totalComponent(), stage2_ff.components().total())
else:
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
stage1_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setFakeGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.add(stage1_fixed_group, MGIdx(1))
stage2_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setFakeGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.add(stage2_fixed_group, MGIdx(1))
else:
stage1_mobile_fixed = GridFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.addFixedAtoms(stage1_fixed_group)
stage2_mobile_fixed = GridFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.addFixedAtoms(stage2_fixed_group)
# forcefield holding the energy between fixed atoms
stage1_mobile_mobile = InterCLJFF("mobile-mobile")
stage1_mobile_mobile = setCLJProperties(stage1_mobile_mobile)
stage1_mobile_mobile.add(stage1_mobile_group)
stage2_mobile_mobile = InterCLJFF("mobile-mobile")
stage2_mobile_mobile = setCLJProperties(stage2_mobile_mobile)
stage2_mobile_mobile.add(stage2_mobile_group)
stage1.add(stage1_mobile_group)
stage1.add(stage1_mobile_fixed)
stage1.add(stage1_mobile_mobile)
stage2.add(stage2_mobile_group)
stage2.add(stage2_mobile_fixed)
stage2.add(stage2_mobile_mobile)
stage1.setComponent(stage1.totalComponent(), stage1_mobile_mobile.components().total() + stage1_mobile_fixed.components().total())
stage2.setComponent(stage2.totalComponent(), stage2_mobile_mobile.components().total() + stage2_mobile_fixed.components().total())
stage1.add(stage1_mobile_group)
stage2.add(stage2_mobile_group)
stage1.add("volume_map", VolMapMonitor(stage1_mobile_group), 1000)
stage2.add("volume_map", VolMapMonitor(stage2_mobile_group), 1000)
max_water_translation = 0.15 * angstroms
max_water_rotation = 15 * degrees
stage1_moves = WeightedMoves()
if stage1_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage1_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage1.containsProperty("reflection sphere radius"):
reflection_radius = float(str(stage1.property("reflection sphere radius"))) * angstroms
reflection_center = stage1.property("reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage1_moves.add(rb_moves, stage1_mobile_group.nViews())
stage2_moves = WeightedMoves()
if stage2_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage2_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage2.containsProperty("reflection sphere radius"):
reflection_radius = float(str(stage2.property("reflection sphere radius"))) * angstroms
reflection_center = stage2.property("reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage2_moves.add(rb_moves, stage2_mobile_group.nViews())
stage1_moves.setTemperature(temperature.val)
stage2_moves.setTemperature(temperature.val)
seed = random_seed.val
if seed is None:
seed = RanGenerator().randInt(100000,1000000)
print("Using generated random number seed %d" % seed)
else:
print("Using supplied random number seed %d" % seed)
stage1_moves.setGenerator( RanGenerator(seed) )
stage2_moves.setGenerator( RanGenerator(seed+7) )
return ( (stage1,stage1_moves), (stage2,stage2_moves) )
def test_nrg(verbose=False):
top_file = "../io/ose.top"
crd_file = "../io/ose.crd"
amber = Amber()
molecules, space = amber.readCrdTop(crd_file, top_file)
# Overload, we want to calc the energy in a non periodic box for comparison with Sander
space = Cartesian()
moleculeNumbers = molecules.molNums()
moleculeList = []
for moleculeNumber in moleculeNumbers:
molecule = molecules.molecule(moleculeNumber).molecule()
moleculeList.append(molecule)
system = System()
solute = MoleculeGroup("solute", moleculeList[0])
# Add these groups to the System
system.add(solute)
# Now solute bond, angle, dihedral energy
solute_intraff = InternalFF("solute_intraff")
solute_intraff.add(solute)
# Now solute intramolecular CLJ energy
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj.add(solute)
# Here is the list of all forcefields
forcefields = [solute_intraff, solute_intraclj]
# Add these forcefields to the system
for forcefield in forcefields:
system.add(forcefield)
system.setProperty("space", space)
system.setProperty(
"switchingFunction",
HarmonicSwitchingFunction(coulomb_cutoff, coulomb_feather, lj_cutoff,
lj_feather))
system.setProperty("combiningRules", VariantProperty(combining_rules))
total_nrg = solute_intraclj.components().total(
) + solute_intraff.components().total()
e_total = system.totalComponent()
system.setComponent(e_total, total_nrg)
if verbose:
print("\nTotal energy ")
print(system.energy())
print("Components energies ")
for component in list(system.energyComponents().keys()):
print(component,
system.energyComponents().value(component) * kcal_per_mol)
print("The AMBER14/sander energies for this system are ")
print("""
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.4880E+01 1.3388E+01 6.2845E+01 C2 20
BOND = 5.1844 ANGLE = 10.0783 DIHED = 20.1271
VDWAALS = -1.7278 EEL = -256.9757 HBOND = 0.0000
1-4 VDW = 10.6377 1-4 EEL = 177.7958 RESTRAINT = 0.0000
""")
diff = abs(-34.880 - system.energy().value())
print("Difference = %s" % diff)
e_bond = system.energy(solute_intraff.components().bond()).value()
e_ang = system.energy(solute_intraff.components().angle()).value()
e_dih = system.energy( solute_intraff.components().dihedral() ).value() + \
system.energy( solute_intraff.components().improper() ).value()
assert_almost_equal(e_bond, 5.1844, 2)
assert_almost_equal(e_ang, 10.0783, 2)
assert_almost_equal(e_dih, 20.1271, 2)
e_coul = system.energy(solute_intraclj.components().coulomb()).value()
e_lj = system.energy(solute_intraclj.components().lj()).value()
assert_almost_equal(e_coul, -256.9757 + 177.7958, 2)
assert_almost_equal(e_lj, -1.7278 + 10.6377, 2)
assert_almost_equal(system.energy().value(), -34.880, 2)
# create the periodic box space for the atoms
box = PeriodicBox(
Vector(box_size[0].value(), box_size[1].value(), box_size[2].value()))
# create a forcefield to calculate the intermolecular coulomb and LJ (CLJ)
# energy between all krypton atoms
interff = InterCLJFF("CLJ")
interff.setProperty("space", box)
interff.add(mols)
# create a simulation system to hold the forcefield and atoms
system = System()
system.add(interff)
system.add(mols)
system.setProperty("space", box)
# add a wrapper that wraps the atoms back into the box
system.add(SpaceWrapper(Vector(0), mols))
# create rigid body translation moves for the atoms
rb_moves = RigidBodyMC(mols)
rb_moves.setMaximumTranslation(max_translate)
rb_moves.setTemperature(temperature)
# create volume moves to change the box size
vol_moves = VolumeMove(mols)
vol_moves.setMaximumVolumeChange(mols.nMolecules() * 0.1 * angstrom3)
vol_moves.setTemperature(temperature)
vol_moves.setPressure(pressure)
def test_props(verbose=False):
sys = System()
box0 = PeriodicBox( Vector(10.0,10.0,10.0) )
box1 = PeriodicBox( Vector(20.0,20.0,20.0) )
if verbose:
print(box0)
print(box0.volume())
print(box1.volume())
assert(not sys.containsProperty("space"))
sys.add( InterCLJFF("cljff") )
if verbose:
print(sys)
print(sys.property("space"))
print(sys.userProperties().propertyKeys())
print(sys.builtinProperties().propertyKeys())
assert(sys.containsProperty("space"))
assert_equal( sys.property("space"), Cartesian() )
sys.setProperty( "space0", LinkToProperty("space", FFIdx(0)) )
if verbose:
print(sys.property("space0"))
assert(sys.containsProperty("space0"))
sys.setProperty("space0", box0)
if verbose:
print(sys.property("space"))
assert_equal(sys.property("space0"), box0)
sys.setProperty("space1", box1)
sys.setProperty("combined_space", CombineSpaces("space0", "space1"))
assert_equal(sys.property("space1"), box1)
if verbose:
print(sys.properties().propertyKeys())
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
assert_almost_equal( sys.property("combined_space").volume().value(),
sys.property("space0").volume().value() + sys.property("space1").volume().value(), 5 )
space3 = PeriodicBox( Vector(5,5,5) )
sys.setProperty("space0", space3)
assert_equal( sys.property("space0"), space3 )
if verbose:
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
assert_almost_equal( sys.property("combined_space").volume().value(),
sys.property("space0").volume().value() + sys.property("space1").volume().value(), 5 )
sys.removeProperty("space0")
if verbose:
print(sys.properties().propertyKeys())
assert( not sys.containsProperty("space0") )
salt.add(m1)
salt.add(m2)
salt.add(m3)
#salt.add(c)
#salt.add(c2)
cljff = InterCLJFF("salt-salt")
cljff.add(salt)
internalff.add(salt)
system = System()
system.add(salt)
system.add(cljff)
system.add(internalff)
system.setProperty("space", PeriodicBox( Vector(20,20,20) ) )
system.add( SpaceWrapper(Vector(0,0,0),salt) )
t.start()
print("Initial energy = %s" % system.energy())
print("(took %d ms)" % t.elapsed())
mdmove = MolecularDynamics( salt, VelocityVerlet(),
{"velocity generator":MaxwellBoltzmann(25*celsius)} )
mdmove = MolecularDynamics(salt, DLMRigidBody() )
mdmove.setTimeStep(1*femtosecond)
do_mc = False
def createSystemFrom(molecules,
space,
system_name,
naming_scheme=NamingScheme()):
"""Create a new System from the passed molecules and space,
sorting the molecules into different molecule groups based on the
passed naming scheme"""
system = System(system_name)
# If requested, change the water model for all water molecules
if water_model.val == "tip4p":
molnums = molecules.molNums()
new_molecules = Molecules()
print("Forcing all water molecules to use the %s water model..." %
water_model.val)
print("Converting %d molecules..." % len(molnums))
i = 0
for molnum in molnums:
molecule = molecules[molnum].molecule()
if i % 100 == 0:
print("%d" % i)
sys.stdout.flush()
elif i % 10 == 0:
print(".", end=' ')
sys.stdout.flush()
i += 1
if molecule.nAtoms() == 3:
# this could be a TIP3P water
resname = str(molecule.residue().name().value()).lower()
if resname == "wat" or resname == "t3p":
new_molecule = convertTip3PtoTip4P(molecule)
if new_molecule:
molecule = new_molecule
new_molecules.add(molecule)
print("%d" % i)
molecules = new_molecules
nmols = molecules.nMolecules()
print("Number of molecules == %s" % nmols)
print("System space == %s" % space)
if nmols == 0:
return system
print("Assigning molecules to molecule groups...")
solute_group = MoleculeGroup(naming_scheme.solutesGroupName().value())
protein_group = MoleculeGroup(naming_scheme.proteinsGroupName().value())
solvent_group = MoleculeGroup(naming_scheme.solventsGroupName().value())
water_group = MoleculeGroup(naming_scheme.watersGroupName().value())
ion_group = MoleculeGroup(naming_scheme.ionsGroupName().value())
all_group = MoleculeGroup(naming_scheme.allMoleculesGroupName().value())
# The all molecules group has all of the molecules
all_group.add(molecules)
system.add(all_group)
# Run through each molecule and decide what type it is...
molnums = molecules.molNums()
molnums.sort()
central_molecule = None
solutes = []
proteins = []
solvents = []
waters = []
ions = []
for molnum in molnums:
molecule = molecules[molnum].molecule()
resnams = getResidueNames(molecule)
if naming_scheme.isSolute(resnams):
solutes.append(molecule)
elif naming_scheme.isProtein(resnams):
proteins.append(molecule)
elif naming_scheme.isWater(resnams):
waters.append(molecule)
elif naming_scheme.isIon(resnams):
ions.append(molecule)
elif molecule.nResidues() == 1:
solvents.append(molecule)
else:
solutes.append(molecule)
# Ok - we have now divided everything up into groups
for solute in solutes:
solute_group.add(solute)
for protein in proteins:
protein_group.add(protein)
for water in waters:
solvent_group.add(water)
water_group.add(water)
for solvent in solvents:
solvent_group.add(solvent)
for ion in ions:
solvent_group.add(ion)
ion_group.add(ion)
if solute_group.nMolecules() > 0:
system.add(solute_group)
if protein_group.nMolecules() > 0:
system.add(protein_group)
if solvent_group.nMolecules() > 0:
system.add(solvent_group)
if water_group.nMolecules() > 0:
system.add(water_group)
if ion_group.nMolecules() > 0:
system.add(ion_group)
print("Number of solute molecules == %s" % solute_group.nMolecules())
print("Number of protein molecules == %s" % protein_group.nMolecules())
print("Number of ions == %s" % ion_group.nMolecules())
print("Number of water molecules == %s" % water_group.nMolecules())
print("Number of solvent molecules == %s" % solvent_group.nMolecules())
print(
"(solvent group is waters + ions + unidentified single-residue molecules)"
)
system.setProperty("space", space)
system.add(SpaceWrapper(Vector(0), all_group))
system.applyConstraints()
print("Returning the constructed system")
return system
def makeSim(system, ligand_mol, watersys):
"""Create simulation systems with and without the ligand and return those systems together
with the moves"""
stage1 = System("with_ligand")
stage2 = System("without_ligand")
if system.containsProperty("reflection center"):
reflection_center = system.property("reflection center").toVector()[0]
reflection_radius = float(
str(system.property("reflection sphere radius")))
stage1.setProperty("reflection center",
AtomCoords(CoordGroup(1, reflection_center)))
stage1.setProperty("reflection sphere radius",
VariantProperty(reflection_radius))
stage2.setProperty("reflection center",
AtomCoords(CoordGroup(1, reflection_center)))
stage2.setProperty("reflection sphere radius",
VariantProperty(reflection_radius))
# create a molecule group for fixed atoms (everything except the mobile water)
fixed_group = MoleculeGroup("fixed")
if MGName("fixed_molecules") in system.mgNames():
fixed_group.add(system[MGName("fixed_molecules")])
if MGName("mobile_solutes") in system.mgNames():
fixed_group.add(system[MGName("mobile_solutes")])
if MGName("protein_sidechains") in system.mgNames() or \
MGName("protein_backbones") in system.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = system[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
pass
try:
protein_backbones = system[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
pass
try:
boundary_molecules = system[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
pass
for molnum in all_proteins.molNums():
protein_mol = Molecule.join(all_proteins[molnum])
fixed_group.add(protein_mol)
stage1_fixed_group = MoleculeGroup(fixed_group)
stage2_fixed_group = MoleculeGroup(fixed_group)
stage1_fixed_group.add(ligand_mol)
stage2_fixed_group.remove(ligand_mol)
mobile_group = MoleculeGroup("mobile_group")
if MGName("mobile_solvents") in system.mgNames():
mobile_group.add(system[MGName("mobile_solvents")])
stage1_mobile_group = MoleculeGroup(mobile_group)
stage2_mobile_group = MoleculeGroup(mobile_group)
# now find water molecules from the water system that can be substituted for the ligand
watermols = findOverlappingWaters(ligand_mol, watersys)
stage2_mobile_group.add(watermols)
print("The number of stage 1 fixed non-solvent molecules is %d." %
stage1_fixed_group.nMolecules())
print("The number of stage 1 mobile solvent molecules is %d." %
stage1_mobile_group.nMolecules())
print("The number of stage 2 fixed non-solvent molecules is %d." %
stage2_fixed_group.nMolecules())
print("The number of stage 2 mobile solvent molecules is %d." %
stage2_mobile_group.nMolecules())
# write a PDB of all of the fixed molecules
PDB().write(stage1_mobile_group, "stage1_mobile_atoms.pdb")
PDB().write(stage2_mobile_group, "stage2_mobile_atoms.pdb")
PDB().write(stage1_fixed_group, "stage1_fixed_atoms.pdb")
PDB().write(stage2_fixed_group, "stage2_fixed_atoms.pdb")
# create the forcefields
if use_fast_ff.val:
stage1_ff = InterFF("ff")
stage2_ff = InterFF("ff")
stage1_ff.setCLJFunction(
CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val))
stage2_ff.setCLJFunction(
CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val))
if disable_grid.val:
stage1_ff.disableGrid()
stage2_ff.disableGrid()
else:
stage1_ff.enableGrid()
stage1_ff.setGridSpacing(grid_spacing.val)
stage1_ff.setGridBuffer(grid_buffer.val)
stage2_ff.enableGrid()
stage2_ff.setGridSpacing(grid_spacing.val)
stage2_ff.setGridBuffer(grid_buffer.val)
stage1_ff.add(stage1_mobile_group)
stage1_ff.setFixedAtoms(stage1_fixed_group.molecules())
stage2_ff.add(stage2_mobile_group)
stage2_ff.setFixedAtoms(stage2_fixed_group.molecules())
stage1.add(stage1_ff)
stage1.setComponent(stage1.totalComponent(),
stage1_ff.components().total())
stage2.add(stage1_ff)
stage2.setComponent(stage2.totalComponent(),
stage2_ff.components().total())
else:
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
stage1_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setFakeGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.add(stage1_fixed_group, MGIdx(1))
stage2_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setFakeGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.add(stage2_fixed_group, MGIdx(1))
else:
stage1_mobile_fixed = GridFF2("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.addFixedAtoms(stage1_fixed_group)
stage2_mobile_fixed = GridFF2("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.addFixedAtoms(stage2_fixed_group)
# forcefield holding the energy between fixed atoms
stage1_mobile_mobile = InterCLJFF("mobile-mobile")
stage1_mobile_mobile = setCLJProperties(stage1_mobile_mobile)
stage1_mobile_mobile.add(stage1_mobile_group)
stage2_mobile_mobile = InterCLJFF("mobile-mobile")
stage2_mobile_mobile = setCLJProperties(stage2_mobile_mobile)
stage2_mobile_mobile.add(stage2_mobile_group)
stage1.add(stage1_mobile_group)
stage1.add(stage1_mobile_fixed)
stage1.add(stage1_mobile_mobile)
stage2.add(stage2_mobile_group)
stage2.add(stage2_mobile_fixed)
stage2.add(stage2_mobile_mobile)
stage1.setComponent(
stage1.totalComponent(),
stage1_mobile_mobile.components().total() +
stage1_mobile_fixed.components().total())
stage2.setComponent(
stage2.totalComponent(),
stage2_mobile_mobile.components().total() +
stage2_mobile_fixed.components().total())
stage1.add(stage1_mobile_group)
stage2.add(stage2_mobile_group)
stage1.add("volume_map", VolMapMonitor(stage1_mobile_group), 1000)
stage2.add("volume_map", VolMapMonitor(stage2_mobile_group), 1000)
max_water_translation = 0.15 * angstroms
max_water_rotation = 15 * degrees
stage1_moves = WeightedMoves()
if stage1_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage1_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage1.containsProperty("reflection sphere radius"):
reflection_radius = float(
str(stage1.property("reflection sphere radius"))) * angstroms
reflection_center = stage1.property(
"reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage1_moves.add(rb_moves, stage1_mobile_group.nViews())
stage2_moves = WeightedMoves()
if stage2_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage2_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage2.containsProperty("reflection sphere radius"):
reflection_radius = float(
str(stage2.property("reflection sphere radius"))) * angstroms
reflection_center = stage2.property(
"reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage2_moves.add(rb_moves, stage2_mobile_group.nViews())
stage1_moves.setTemperature(temperature.val)
stage2_moves.setTemperature(temperature.val)
seed = random_seed.val
if seed is None:
seed = RanGenerator().randInt(100000, 1000000)
print("Using generated random number seed %d" % seed)
else:
print("Using supplied random number seed %d" % seed)
stage1_moves.setGenerator(RanGenerator(seed))
stage2_moves.setGenerator(RanGenerator(seed + 7))
return ((stage1, stage1_moves), (stage2, stage2_moves))
switchfunc = HarmonicSwitchingFunction(10*angstrom, 9.5*angstrom)
system = System()
for forcefield in forcefields:
forcefield.add(waters)
system.add(forcefield)
def printEnergies(nrgs):
keys = list(nrgs.keys())
keys.sort()
for key in keys:
print("%25s : %12.8f" % (key, nrgs[key]))
system.setProperty("space", space)
system.setProperty("switchingFunction", switchfunc)
printEnergies(system.energies())
print("\nEnergy with respect to cutoff length\n")
print(" Distance Group Shifted ReactionField Atomistic")
for i in range(10,200,5):
x = i*0.1
switchfunc = HarmonicSwitchingFunction(x*angstrom, (x-0.5)*angstrom)
system.setProperty("switchingFunction", switchfunc)
print("%12.8f %12.8f %12.8f %12.8f %12.8f" % (x, system.energy(group_coul).value(),
system.energy(shift_coul).value(), system.energy(field_coul).value(),
box0 = PeriodicBox( Vector(10.0,10.0,10.0) )
box1 = PeriodicBox( Vector(20.0,20.0,20.0) )
print(box0)
print(box0.volume())
print(box1.volume())
from Sire.MM import *
sys.add( InterCLJFF("cljff") )
print(sys)
print(sys.property("space"))
print(sys.userProperties().propertyKeys())
print(sys.builtinProperties().propertyKeys())
sys.setProperty( "space0", LinkToProperty("space", FFIdx(0)) )
print(sys.property("space0"))
sys.setProperty("space0", box0)
print(sys.property("space"))
sys.setProperty("space1", box1)
sys.setProperty("combined_space", CombineSpaces("space0", "space1"))
print(sys.properties().propertyKeys())
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
def createSystemFrom(molecules, space, system_name, naming_scheme = NamingScheme()):
"""Create a new System from the passed molecules and space,
sorting the molecules into different molecule groups based on the
passed naming scheme"""
system = System(system_name)
# If requested, change the water model for all water molecules
if water_model.val == "tip4p":
molnums = molecules.molNums()
new_molecules = Molecules()
print("Forcing all water molecules to use the %s water model..." % water_model.val)
print("Converting %d molecules..." % len(molnums))
i = 0
for molnum in molnums:
molecule = molecules[molnum].molecule()
if i % 100 == 0:
print("%d" % i)
sys.stdout.flush()
elif i % 10 == 0:
print(".", end=' ')
sys.stdout.flush()
i += 1
if molecule.nAtoms() == 3:
# this could be a TIP3P water
resname =str(molecule.residue().name().value()).lower()
if resname == "wat" or resname == "t3p":
new_molecule = convertTip3PtoTip4P(molecule)
if new_molecule:
molecule = new_molecule
new_molecules.add(molecule)
print("%d" % i)
molecules = new_molecules
nmols = molecules.nMolecules()
print("Number of molecules == %s" % nmols)
print("System space == %s" % space)
if nmols == 0:
return system
print("Assigning molecules to molecule groups...")
solute_group = MoleculeGroup(naming_scheme.solutesGroupName().value())
protein_group = MoleculeGroup(naming_scheme.proteinsGroupName().value())
solvent_group = MoleculeGroup(naming_scheme.solventsGroupName().value())
water_group = MoleculeGroup(naming_scheme.watersGroupName().value())
ion_group = MoleculeGroup(naming_scheme.ionsGroupName().value())
all_group = MoleculeGroup(naming_scheme.allMoleculesGroupName().value())
# The all molecules group has all of the molecules
all_group.add(molecules)
system.add(all_group)
# Run through each molecule and decide what type it is...
molnums = molecules.molNums()
molnums.sort()
central_molecule = None
solutes = []
proteins = []
solvents = []
waters = []
ions = []
for molnum in molnums:
molecule = molecules[molnum].molecule()
resnams = getResidueNames(molecule)
if naming_scheme.isSolute(resnams):
solutes.append(molecule)
elif naming_scheme.isProtein(resnams):
proteins.append(molecule)
elif naming_scheme.isWater(resnams):
waters.append(molecule)
elif naming_scheme.isIon(resnams):
ions.append(molecule)
elif molecule.nResidues() == 1:
solvents.append(molecule)
else:
solutes.append(molecule)
# Ok - we have now divided everything up into groups
for solute in solutes:
solute_group.add(solute)
for protein in proteins:
protein_group.add(protein)
for water in waters:
solvent_group.add(water)
water_group.add(water)
for solvent in solvents:
solvent_group.add(solvent)
for ion in ions:
solvent_group.add(ion)
ion_group.add(ion)
if solute_group.nMolecules() > 0:
system.add(solute_group)
if protein_group.nMolecules() > 0:
system.add(protein_group)
if solvent_group.nMolecules() > 0:
system.add(solvent_group)
if water_group.nMolecules() > 0:
system.add(water_group)
if ion_group.nMolecules() > 0:
system.add(ion_group)
print("Number of solute molecules == %s" % solute_group.nMolecules())
print("Number of protein molecules == %s" % protein_group.nMolecules())
print("Number of ions == %s" % ion_group.nMolecules())
print("Number of water molecules == %s" % water_group.nMolecules())
print("Number of solvent molecules == %s" % solvent_group.nMolecules())
print("(solvent group is waters + ions + unidentified single-residue molecules)")
system.setProperty("space", space)
system.add( SpaceWrapper( Vector(0), all_group ) )
system.applyConstraints()
print("Returning the constructed system")
return system
system = System()
system.add(solute)
system.add(solvent)
solvent_cljff = InterCLJFF("solvent_cljff")
solvent_cljff.add(solvent)
solute_solvent_cljff = InterGroupCLJFF("solute_solvent_cljff")
solute_solvent_cljff.add(solute, MGIdx(0))
solute_solvent_cljff.add(solvent, MGIdx(1))
system.add(solvent_cljff)
system.add(solute_solvent_cljff)
system.setProperty(
"space",
PeriodicBox(Vector(-18.3854, -18.66855, -18.4445),
Vector(18.3854, 18.66855, 18.4445)))
print("Equilibrating the system...")
solvent_move = RigidBodyMC(
PrefSampler(solute.moleculeAt(0), solvent, 200 * angstrom2))
solvent_move.setMaximumTranslation(0.2 * angstrom)
solvent_move.setMaximumRotation(5 * degrees)
solute_move = RigidBodyMC(solute)
solute_move.setMaximumTranslation(0.2 * angstrom)
solute_move.setMaximumRotation(5 * degrees)
moves = WeightedMoves()
moves.add(solvent_move, 100)
box0 = PeriodicBox(Vector(10.0, 10.0, 10.0))
box1 = PeriodicBox(Vector(20.0, 20.0, 20.0))
print(box0)
print(box0.volume())
print(box1.volume())
from Sire.MM import *
sys.add(InterCLJFF("cljff"))
print(sys)
print(sys.property("space"))
print(sys.userProperties().propertyKeys())
print(sys.builtinProperties().propertyKeys())
sys.setProperty("space0", LinkToProperty("space", FFIdx(0)))
print(sys.property("space0"))
sys.setProperty("space0", box0)
print(sys.property("space"))
sys.setProperty("space1", box1)
sys.setProperty("combined_space", CombineSpaces("space0", "space1"))
print(sys.properties().propertyKeys())
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
# create the periodic box space for the atoms
box = PeriodicBox( Vector(box_size[0].value(),
box_size[1].value(),
box_size[2].value()) )
# create a forcefield to calculate the intermolecular coulomb and LJ (CLJ)
# energy between all krypton atoms
interff = InterCLJFF("CLJ")
interff.setProperty("space", box)
interff.add(mols)
# create a simulation system to hold the forcefield and atoms
system = System()
system.add(interff)
system.add(mols)
system.setProperty("space", box)
# add a wrapper that wraps the atoms back into the box
system.add( SpaceWrapper( Vector(0), mols ) )
# create rigid body translation moves for the atoms
rb_moves = RigidBodyMC(mols)
rb_moves.setMaximumTranslation(max_translate)
rb_moves.setTemperature(temperature)
# create volume moves to change the box size
vol_moves = VolumeMove(mols)
vol_moves.setMaximumVolumeChange( mols.nMolecules() * 0.1 * angstrom3 )
vol_moves.setTemperature(temperature)
vol_moves.setPressure(pressure)
def createSystem():
protomsdir = "%s/Work/ProtoMS" % os.getenv("HOME")
protoms = ProtoMS("%s/protoms2" % protomsdir)
protoms.addParameterFile("%s/parameter/amber99.ff" % protomsdir)
protoms.addParameterFile("%s/parameter/solvents.ff" % protomsdir)
protoms.addParameterFile("%s/parameter/gaff.ff" % protomsdir)
protoms.addParameterFile(solute_params)
solute = PDB().readMolecule(solute_file)
solute = solute.edit().rename(solute_name).commit()
solute = protoms.parameterise(solute, ProtoMS.SOLUTE)
perturbation = solute.property("perturbations")
lam = Symbol("lambda")
lam_fwd = Symbol("lambda_{fwd}")
lam_bwd = Symbol("lambda_{bwd}")
initial = Perturbation.symbols().initial()
final = Perturbation.symbols().final()
solute = solute.edit().setProperty(
"perturbations",
perturbation.recreate((1 - lam) * initial + lam * final)).commit()
solute_fwd = solute.edit().renumber().setProperty(
"perturbations", perturbation.substitute(lam, lam_fwd)).commit()
solute_bwd = solute.edit().renumber().setProperty(
"perturbations", perturbation.substitute(lam, lam_bwd)).commit()
solvent = PDB().read(solvent_file)
tip4p = solvent.moleculeAt(0).molecule()
tip4p = tip4p.edit().rename(solvent_name).commit()
tip4p = protoms.parameterise(tip4p, ProtoMS.SOLVENT)
tip4p_chgs = tip4p.property("charge")
tip4p_ljs = tip4p.property("LJ")
for i in range(0, solvent.nMolecules()):
tip4p = solvent.moleculeAt(i).molecule()
tip4p = tip4p.edit().rename(solvent_name) \
.setProperty("charge", tip4p_chgs) \
.setProperty("LJ", tip4p_ljs) \
.commit()
solvent.update(tip4p)
system = System()
solutes = MoleculeGroup("solutes")
solutes.add(solute)
solutes.add(solute_fwd)
solutes.add(solute_bwd)
solvent = MoleculeGroup("solvent", solvent)
all = MoleculeGroup("all")
all.add(solutes)
all.add(solvent)
system.add(solutes)
system.add(solvent)
system.add(all)
solventff = InterCLJFF("solvent:solvent")
solventff.add(solvent)
solute_intraff = InternalFF("solute_intraff")
solute_intraff.add(solute)
solute_fwd_intraff = InternalFF("solute_fwd_intraff")
solute_fwd_intraff.add(solute_fwd)
solute_bwd_intraff = InternalFF("solute_bwd_intraff")
solute_bwd_intraff.add(solute_bwd)
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj.add(solute)
solute_fwd_intraclj = IntraCLJFF("solute_fwd_intraclj")
solute_fwd_intraclj.add(solute_fwd)
solute_bwd_intraclj = IntraCLJFF("solute_bwd_intraclj")
solute_bwd_intraclj.add(solute_bwd)
solute_solventff = InterGroupCLJFF("solute:solvent")
solute_solventff.add(solute, MGIdx(0))
solute_solventff.add(solvent, MGIdx(1))
solute_fwd_solventff = InterGroupCLJFF("solute_fwd:solvent")
solute_fwd_solventff.add(solute_fwd, MGIdx(0))
solute_fwd_solventff.add(solvent, MGIdx(1))
solute_bwd_solventff = InterGroupCLJFF("solute_bwd:solvent")
solute_bwd_solventff.add(solute_bwd, MGIdx(0))
solute_bwd_solventff.add(solvent, MGIdx(1))
forcefields = [
solventff, solute_intraff, solute_intraclj, solute_solventff,
solute_fwd_intraff, solute_fwd_intraclj, solute_fwd_solventff,
solute_bwd_intraff, solute_bwd_intraclj, solute_bwd_solventff
]
for forcefield in forcefields:
system.add(forcefield)
xsc_line = open(solvent_file, "r").readlines()[0]
words = xsc_line.split()
#HEADER box -12.5 -12.5 -12.5 12.5 12.5 12.5
space = PeriodicBox(
Vector(float(words[2]), float(words[3]), float(words[4])),
Vector(float(words[5]), float(words[6]), float(words[7])))
system.setProperty("space", space)
system.setProperty(
"switchingFunction",
HarmonicSwitchingFunction(coulomb_cutoff, coulomb_feather, lj_cutoff,
lj_feather))
system.setProperty("combiningRules", VariantProperty(combining_rules))
e_total = system.totalComponent()
e_fwd = Symbol("E_{fwd}")
e_bwd = Symbol("E_{bwd}")
total_nrg = solventff.components().total() + \
solute_intraclj.components().total() + solute_intraff.components().total() + \
solute_solventff.components().total()
fwd_nrg = solventff.components().total() + \
solute_fwd_intraclj.components().total() + solute_fwd_intraff.components().total() + \
solute_fwd_solventff.components().total()
bwd_nrg = solventff.components().total() + \
solute_bwd_intraclj.components().total() + solute_bwd_intraff.components().total() + \
solute_bwd_solventff.components().total()
system.setComponent(e_total, total_nrg)
system.setComponent(e_fwd, fwd_nrg)
system.setComponent(e_bwd, bwd_nrg)
system.setConstant(lam, 0.0)
system.setConstant(lam_fwd, 0.0)
system.setConstant(lam_bwd, 0.0)
system.add(SpaceWrapper(Vector(0, 0, 0), all))
system.add(PerturbationConstraint(solutes))
system.add(ComponentConstraint(lam_fwd, Min(lam + delta_lambda, 1)))
system.add(ComponentConstraint(lam_bwd, Max(lam - delta_lambda, 0)))
de_fwd = Symbol("de_fwd")
de_bwd = Symbol("de_bwd")
system.setComponent(de_fwd, fwd_nrg - total_nrg)
system.setComponent(de_bwd, total_nrg - bwd_nrg)
system.add("total_energy", MonitorComponent(e_total, Average()))
system.add("de_fwd",
MonitorComponent(de_fwd, FreeEnergyAverage(temperature)))
system.add("de_bwd",
MonitorComponent(de_bwd, FreeEnergyAverage(temperature)))
system.setComponent(lam, 0.0)
print "LAMBDA=0 : Energy = %f kcal mol-1" % system.energy().to(
kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
system.setComponent(lam, 0.5)
print "LAMBDA=0.5 : Energy = %f kcal mol-1" % system.energy().to(
kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
system.setComponent(lam, 1.0)
print "LAMBDA=1.0 : Energy = %f kcal mol-1" % system.energy().to(
kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
return system
field_coul = field_clj.components().coulomb()
system = System()
for forcefield in forcefields:
forcefield.add(protein)
system.add(forcefield)
def printEnergies(nrgs):
keys = list(nrgs.keys())
keys.sort()
for key in keys:
print("%25s : %12.8f" % (key, nrgs[key]))
system.setProperty("switchingFunction", HarmonicSwitchingFunction(10*angstrom, 9.5*angstrom))
printEnergies(system.energies())
print("\nEnergy with respect to cutoff length\n")
print(" Distance Group Shifted ReactionField ")
for i in range(10,501,5):
x = i*0.1
switchfunc = HarmonicSwitchingFunction(x*angstrom, (x-0.5)*angstrom)
system.setProperty("switchingFunction", switchfunc)
print("%12.8f %12.8f %12.8f %12.8f" % (x, system.energy(group_coul).value(),
system.energy(shift_coul).value(), system.energy(field_coul).value()))
titrator.setNegativeTemplate(chloride)
titrator.setNeutralTemplate(water)
system = System()
cljff = InterCLJFF("cljff")
cljff.add(molecules)
solvent = MoleculeGroup("solvent")
solvent.add(molecules)
titrator.setMoleculeGroup(solvent)
system.add(cljff)
system.add(solvent)
system.setProperty("space", space)
print("Initialising the ions...")
titrator.applyTo(system)
print("Randomising the location of ions...")
titrator.randomiseCharge(3)
titrator.applyTo(system)
print("System is ready for simulation :-)")
PDB().write(system.molecules(), "test0000.pdb")
move = TitrationMove()
move.setTemperature(25 * celsius)
moves = WeightedMoves()
moves.add(move, 1)
def createSystem():
protomsdir = "%s/Work/ProtoMS" % os.getenv("HOME")
protoms = ProtoMS( "%s/protoms2" % protomsdir )
protoms.addParameterFile( "%s/parameter/amber99.ff" % protomsdir )
protoms.addParameterFile( "%s/parameter/solvents.ff" % protomsdir )
protoms.addParameterFile( "%s/parameter/gaff.ff" % protomsdir )
protoms.addParameterFile( solute_params )
solute = PDB().readMolecule(solute_file)
solute = solute.edit().rename(solute_name).commit()
solute = protoms.parameterise(solute, ProtoMS.SOLUTE)
perturbation = solute.property("perturbations")
lam = Symbol("lambda")
lam_fwd = Symbol("lambda_{fwd}")
lam_bwd = Symbol("lambda_{bwd}")
initial = Perturbation.symbols().initial()
final = Perturbation.symbols().final()
solute = solute.edit().setProperty("perturbations",
perturbation.recreate( (1-lam)*initial + lam*final ) ).commit()
solute_fwd = solute.edit().renumber().setProperty("perturbations",
perturbation.substitute( lam, lam_fwd ) ).commit()
solute_bwd = solute.edit().renumber().setProperty("perturbations",
perturbation.substitute( lam, lam_bwd ) ).commit()
solvent = PDB().read(solvent_file)
tip4p = solvent.moleculeAt(0).molecule()
tip4p = tip4p.edit().rename(solvent_name).commit()
tip4p = protoms.parameterise(tip4p, ProtoMS.SOLVENT)
tip4p_chgs = tip4p.property("charge")
tip4p_ljs = tip4p.property("LJ")
for i in range(0,solvent.nMolecules()):
tip4p = solvent.moleculeAt(i).molecule()
tip4p = tip4p.edit().rename(solvent_name) \
.setProperty("charge", tip4p_chgs) \
.setProperty("LJ", tip4p_ljs) \
.commit()
solvent.update(tip4p)
system = System()
solutes = MoleculeGroup("solutes")
solutes.add(solute)
solutes.add(solute_fwd)
solutes.add(solute_bwd)
solvent = MoleculeGroup("solvent", solvent)
all = MoleculeGroup("all")
all.add(solutes)
all.add(solvent)
system.add(solutes)
system.add(solvent)
system.add(all)
solventff = InterCLJFF("solvent:solvent")
solventff.add(solvent)
solute_intraff = InternalFF("solute_intraff")
solute_intraff.add(solute)
solute_fwd_intraff = InternalFF("solute_fwd_intraff")
solute_fwd_intraff.add(solute_fwd)
solute_bwd_intraff = InternalFF("solute_bwd_intraff")
solute_bwd_intraff.add(solute_bwd)
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj.add(solute)
solute_fwd_intraclj = IntraCLJFF("solute_fwd_intraclj")
solute_fwd_intraclj.add(solute_fwd)
solute_bwd_intraclj = IntraCLJFF("solute_bwd_intraclj")
solute_bwd_intraclj.add(solute_bwd)
solute_solventff = InterGroupCLJFF("solute:solvent")
solute_solventff.add(solute, MGIdx(0))
solute_solventff.add(solvent, MGIdx(1))
solute_fwd_solventff = InterGroupCLJFF("solute_fwd:solvent")
solute_fwd_solventff.add(solute_fwd, MGIdx(0))
solute_fwd_solventff.add(solvent, MGIdx(1))
solute_bwd_solventff = InterGroupCLJFF("solute_bwd:solvent")
solute_bwd_solventff.add(solute_bwd, MGIdx(0))
solute_bwd_solventff.add(solvent, MGIdx(1))
forcefields = [ solventff, solute_intraff, solute_intraclj, solute_solventff,
solute_fwd_intraff, solute_fwd_intraclj, solute_fwd_solventff,
solute_bwd_intraff, solute_bwd_intraclj, solute_bwd_solventff ]
for forcefield in forcefields:
system.add(forcefield)
xsc_line = open(solvent_file, "r").readlines()[0]
words = xsc_line.split()
#HEADER box -12.5 -12.5 -12.5 12.5 12.5 12.5
space = PeriodicBox( Vector( float(words[2]), float(words[3]), float(words[4]) ),
Vector( float(words[5]), float(words[6]), float(words[7]) ) )
system.setProperty( "space", space )
system.setProperty( "switchingFunction",
HarmonicSwitchingFunction(coulomb_cutoff, coulomb_feather,
lj_cutoff, lj_feather) )
system.setProperty( "combiningRules", VariantProperty(combining_rules) )
e_total = system.totalComponent()
e_fwd = Symbol("E_{fwd}")
e_bwd = Symbol("E_{bwd}")
total_nrg = solventff.components().total() + \
solute_intraclj.components().total() + solute_intraff.components().total() + \
solute_solventff.components().total()
fwd_nrg = solventff.components().total() + \
solute_fwd_intraclj.components().total() + solute_fwd_intraff.components().total() + \
solute_fwd_solventff.components().total()
bwd_nrg = solventff.components().total() + \
solute_bwd_intraclj.components().total() + solute_bwd_intraff.components().total() + \
solute_bwd_solventff.components().total()
system.setComponent( e_total, total_nrg )
system.setComponent( e_fwd, fwd_nrg )
system.setComponent( e_bwd, bwd_nrg )
system.setConstant(lam, 0.0)
system.setConstant(lam_fwd, 0.0)
system.setConstant(lam_bwd, 0.0)
system.add( SpaceWrapper(Vector(0,0,0), all) )
system.add( PerturbationConstraint(solutes) )
system.add( ComponentConstraint( lam_fwd, Min( lam + delta_lambda, 1 ) ) )
system.add( ComponentConstraint( lam_bwd, Max( lam - delta_lambda, 0 ) ) )
de_fwd = Symbol("de_fwd")
de_bwd = Symbol("de_bwd")
system.setComponent( de_fwd, fwd_nrg - total_nrg )
system.setComponent( de_bwd, total_nrg - bwd_nrg )
system.add( "total_energy", MonitorComponent(e_total, Average()) )
system.add( "de_fwd", MonitorComponent(de_fwd, FreeEnergyAverage(temperature)) )
system.add( "de_bwd", MonitorComponent(de_bwd, FreeEnergyAverage(temperature)) )
system.setComponent(lam, 0.0)
print "LAMBDA=0 : Energy = %f kcal mol-1" % system.energy().to(kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
system.setComponent(lam, 0.5)
print "LAMBDA=0.5 : Energy = %f kcal mol-1" % system.energy().to(kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
system.setComponent(lam, 1.0)
print "LAMBDA=1.0 : Energy = %f kcal mol-1" % system.energy().to(kcal_per_mol)
print " (%f, %f)" % (system.energy(e_fwd).to(kcal_per_mol),
system.energy(e_bwd).to(kcal_per_mol))
return system