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
def _pvt_calculateEnergy(lamval, verbose):
cljff01 = InterGroupCLJFF("cljff01")
cljff02 = InterGroupCLJFF("cljff02")
cljff01.add( water0, MGIdx(0) )
cljff01.add( water1, MGIdx(1) )
cljff02.add( water0, MGIdx(0) )
cljff02.add( water2, MGIdx(1) )
soft_cljff01 = InterGroupSoftCLJFF("soft_cljff01")
soft_cljff02 = InterGroupSoftCLJFF("soft_cljff02")
soft_cljff01.add( water0, MGIdx(0) )
soft_cljff01.add( water1, MGIdx(1) )
soft_cljff02.add( water0, MGIdx(0) )
soft_cljff02.add( water2, MGIdx(1) )
ref = MoleculeGroup("ref", water0)
group_a = MoleculeGroup("group_a", water1)
group_b = MoleculeGroup("group_b", water2)
dlam = 0.001
lamval_f = lamval + dlam
lam = Symbol("lambda")
lam_f = Symbol("lambda_f")
soft_nrg = (1-lam) * soft_cljff01.components().total(0) + lam * soft_cljff02.components().total(0)
soft_nrg_f = (1-lam_f) * soft_cljff01.components().total(1) + lam_f * soft_cljff02.components().total(1)
de_soft = soft_nrg_f - soft_nrg
nrg = ((1-lam) * cljff01.components().total()) + (lam * cljff02.components().total())
nrg_f = ((1-lam_f) * cljff01.components().total()) + (lam_f * cljff02.components().total())
de = nrg_f - nrg
soft_cljff01.setProperty("alpha0", VariantProperty(lamval))
soft_cljff02.setProperty("alpha0", VariantProperty(1-lamval))
soft_cljff01.setProperty("alpha1", VariantProperty(lamval_f))
soft_cljff02.setProperty("alpha1", VariantProperty(1-lamval_f))
soft_cljff01.setProperty("coulombPower", VariantProperty(0))
soft_cljff01.setProperty("shiftDelta", VariantProperty(1.1))
soft_cljff02.setProperty("coulombPower", VariantProperty(0))
soft_cljff02.setProperty("shiftDelta", VariantProperty(1.1))
sys = System()
sys.add(cljff01)
sys.add(cljff02)
sys.add(soft_cljff01)
sys.add(soft_cljff02)
sys.add(ref)
sys.add(group_a)
sys.add(group_b)
sys.setComponent(lam, lamval)
sys.setComponent(lam_f, lamval_f)
sys.setComponent(sys.totalComponent(), nrg)
sys.setComponent(Symbol("E_{total_f}"), nrg_f)
sys.setComponent(Symbol("dE"), de)
sys.setComponent(Symbol("E_soft_{total}"), soft_nrg)
sys.setComponent(Symbol("E_soft_{total_f}"), soft_nrg_f)
sys.setComponent(Symbol("dE_soft"), de_soft)
nrgmon = FreeEnergyMonitor(ref, group_a, group_b)
soft_nrgmon = FreeEnergyMonitor(ref, group_a, group_b)
soft_nrgmon.setCoulombPower(0)
soft_nrgmon.setShiftDelta(1.1)
sys.add( "nrgmon", nrgmon )
sys.add( "soft_nrgmon", soft_nrgmon)
sys.collectStats()
nrgmon = sys[ MonitorName("nrgmon") ]
dg = nrgmon.freeEnergies()[0].average()
soft_nrgmon = sys[ MonitorName("soft_nrgmon") ]
soft_dg = soft_nrgmon.freeEnergies()[0].average()
sys_dg = sys.energy(Symbol("dE")).value()
sys_soft_dg = sys.energy(Symbol("dE_soft")).value()
if verbose:
print("%s : %s versus %s (should be equal)" % (lamval,dg,sys_dg))
print("%s : %s versus %s (should be equal)" % (lamval,soft_dg,sys_soft_dg))
assert_almost_equal(dg, sys_dg, 5)
assert_almost_equal(soft_dg, sys_soft_dg, 5)
# Sire performs simulations on simulation System objects.
# A System groups together all of the molecules, forcefields etc.
# into a single unit
system = System()
system.add(cljff)
# Here we create the equation used to calculate the total energy of the
# system. We define a symbol, lambda, which we use here to scale up and
# down the coulomb component of cljff
lam = Symbol("lambda")
total_nrg = cljff.components().lj() + lam * cljff.components().coulomb()
# Here we tell the system to use our equation to calculate the total
# energy, and we set the value of lambda to 0.5
system.setComponent( system.totalComponent(), total_nrg )
system.setConstant( lam, 0.5 )
# Now we create a MoleculeGroup that groups together all of the
# molecules to be moved
mobile_mols = MoleculeGroup("mobile_molecules")
mobile_mols.add(first_water)
mobile_mols.add(second_water)
# We add the molecule group to the system
system.add(mobile_mols)
# We create a periodic boundaries space, and give it to the system
space = PeriodicBox( Vector(5,5,5) )
system.setProperty( "space", space )
print("Initial energy = %s" % system.energy())
data = save(system)
system = load(data)
print("Saved energy = %s" % system.energy())
mc = RigidBodyMC(cljff.group(MGIdx(0)))
moves = SameMoves(mc)
#give a lambda coordinate that turns off the coulomb energy
lam = Symbol("lambda")
system.setComponent( system.totalComponent(), cljff.components().lj() + \
lam * cljff.components().coulomb() )
system.setComponent(lam, 0.0)
print(system.energies())
system.setComponent(lam, 1.0)
print(system.energies())
#create 5 replicas that map from lambda=0 to lambda=1
replicas = Replicas(system, 5)
replicas.setSubMoves(moves)
replicas.setNSubMoves(1000)
replicas.setLambdaComponent(lam)
for i in range(0, 5):
print("Initial energy = %s" % system.energy())
data = save(system)
system = load(data)
print("Saved energy = %s" % system.energy())
mc = RigidBodyMC(cljff.group(MGIdx(0)))
moves = SameMoves(mc)
#give a lambda coordinate that turns off the coulomb energy
lam = Symbol("lambda")
system.setComponent( system.totalComponent(), cljff.components().lj() + \
lam * cljff.components().coulomb() )
system.setComponent( lam, 0.0 )
print(system.energies())
system.setComponent( lam, 1.0 )
print(system.energies())
#create 5 replicas that map from lambda=0 to lambda=1
replicas = Replicas(system, 5)
replicas.setSubMoves(moves)
replicas.setNSubMoves(1000)
replicas.setLambdaComponent(lam)
for i in range(0, 5):
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
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
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) )
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) )
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)
# Note that tip3p water are likely to have bonds between hydrogen atoms.
PDB().write(all, "out.pdb")
print("The AMBER11/sander energies for this system are ")
.setProperty("charge", charges) \
.setProperty("LJ", ljs) \
.commit()
cljff.add(mol)
ms = t.elapsed()
print(("Parameterised all of the water molecules (in %d ms)!" % ms))
system = System()
system.add(cljff)
lam = Symbol("lambda")
system.setComponent( lam, 0.2 )
system.setComponent( system.totalComponent(), lam * cljff.components().total() )
mc = RigidBodyMC(cljff.group(MGIdx(0)))
moves = SameMoves(mc)
def testStream(c):
t.start()
data = Sire.Stream.save(c)
ms = t.elapsed()
print(("Streaming %s took %d ms" % (c.what(), ms)))
print(("%s takes up %d bytes" % (c.what(),data.size())))
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)
cljff.add(swapwaters, MGIdx(0))
cljff.add(waters, MGIdx(1))
cljff.setSpace( Cartesian() )
cljff.setShiftElectrostatics(True)
swap_swapff = InterCLJFF("swap-swap")
swap_swapff.setSpace(Cartesian())
swap_swapff.setSwitchingFunction( HarmonicSwitchingFunction(25*angstrom, 25*angstrom, 10*angstrom, 10*angstrom) )
swap_swapff.add(swapwaters)
grid_system.add(swap_swapff)
exp_system.add(swap_swapff)
grid_system.add(gridff)
exp_system.add(cljff)
grid_system.setComponent( grid_system.totalComponent(), \
gridff.components().total() + swap_swapff.components().total() )
exp_system.setComponent( exp_system.totalComponent(), \
cljff.components().total() + swap_swapff.components().total() )
print((grid_system.energies()))
print((exp_system.energies()))
print(("\nGrid energy equals: %s. Explicit energy equals: %s." % \
(grid_system.energy(), exp_system.energy())))
diff = grid_system.energy() - exp_system.energy()
print(("The difference is %s\n" % diff))
rbmc = RigidBodyMC(swapwaters)
rbmc.setReflectionSphere(center_point, 7.5*angstrom)
gridff2.setSpace( Cartesian() )
gridff2.setShiftElectrostatics(True)
#gridff2.setUseReactionField(True)
#gridff2.setUseAtomisticCutoff(True)
swap_swapff = InterCLJFF("swap-swap")
swap_swapff.setSpace(Cartesian())
swap_swapff.setSwitchingFunction( HarmonicSwitchingFunction(25*angstrom, 25*angstrom, 10*angstrom, 10*angstrom) )
swap_swapff.add(swapwaters)
grid_system.add(swap_swapff)
grid_system2.add(swap_swapff)
grid_system.add(gridff)
grid_system2.add(gridff2)
grid_system.setComponent( grid_system.totalComponent(), \
gridff.components().total() + swap_swapff.components().total() )
grid_system2.setComponent( grid_system2.totalComponent(), \
gridff2.components().total() + swap_swapff.components().total() )
print(grid_system.energies())
print(grid_system2.energies())
print("\nOld Grid energy equals: %s. New GridFF energy equals: %s." % \
(grid_system.energy(), grid_system2.energy()))
diff = grid_system.energy() - grid_system2.energy()
print("The difference is %s\n" % diff)
rbmc = RigidBodyMC(swapwaters)
rbmc.setReflectionSphere(center_point, 7.5*angstrom)
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
mol = mols.moleculeAt(i).molecule()
mol = mol.edit().rename("T4P") \
.setProperty("charge", charges) \
.setProperty("LJ", ljs) \
.commit()
cljff.add(mol)
system = System()
system.add(cljff)
lam = Symbol("lambda")
system.setComponent( lam, 0.2 )
system.setComponent( system.totalComponent(), lam * cljff.components().total() )
mc = RigidBodyMC(cljff.group(MGIdx(0)))
moves = SameMoves(mc)
def test_stream(verbose=False):
if verbose:
print("saving system...")
data = Sire.Stream.save(system)
if verbose:
print(("%s takes up %d bytes" % (system.what(),data.size())))
residues.add(residue)
# need to calculate required energy using differences as old IntraCLJFF is buggy!
oldsys = System()
oldsys.add(ligmol)
oldsys.add(residues)
oldsys.add(oldff)
oldsys.add(old0ff)
oldsys.add(old1ff)
etotal = Symbol("E_{total}")
ecoul = Symbol("E_{coul}")
elj = Symbol("E_{lj}")
oldsys.setComponent( etotal, oldff.components().total() - \
old0ff.components().total() - \
old1ff.components().total() )
if oldsys.totalComponent() != etotal:
oldsys.setComponent( oldsys.totalComponent(), etotal )
oldsys.setComponent( ecoul, oldff.components().coulomb() - \
old0ff.components().coulomb() - \
old1ff.components().coulomb() )
oldsys.setComponent( elj, oldff.components().lj() - \
old0ff.components().lj() - \
old1ff.components().lj() )
newsys = System()
newsys.add(ligmol)
newsys.add(residues)
def calculateEnergy(lamval):
cljff01 = InterGroupCLJFF("cljff01")
cljff02 = InterGroupCLJFF("cljff02")
cljff01.add(water0, MGIdx(0))
cljff01.add(water1, MGIdx(1))
cljff02.add(water0, MGIdx(0))
cljff02.add(water2, MGIdx(1))
soft_cljff01 = InterGroupSoftCLJFF("soft_cljff01")
soft_cljff02 = InterGroupSoftCLJFF("soft_cljff02")
soft_cljff01.add(water0, MGIdx(0))
soft_cljff01.add(water1, MGIdx(1))
soft_cljff02.add(water0, MGIdx(0))
soft_cljff02.add(water2, MGIdx(1))
ref = MoleculeGroup("ref", water0)
group_a = MoleculeGroup("group_a", water1)
group_b = MoleculeGroup("group_b", water2)
dlam = 0.001
lamval_f = lamval + dlam
lam = Symbol("lambda")
lam_f = Symbol("lambda_f")
soft_nrg = (1 - lam) * soft_cljff01.components().total(
0) + lam * soft_cljff02.components().total(0)
soft_nrg_f = (1 - lam_f) * soft_cljff01.components().total(
1) + lam_f * soft_cljff02.components().total(1)
de_soft = soft_nrg_f - soft_nrg
nrg = ((1 - lam) *
cljff01.components().total()) + (lam * cljff02.components().total())
nrg_f = ((1 - lam_f) * cljff01.components().total()) + (
lam_f * cljff02.components().total())
de = nrg_f - nrg
soft_cljff01.setProperty("alpha0", VariantProperty(lamval))
soft_cljff02.setProperty("alpha0", VariantProperty(1 - lamval))
soft_cljff01.setProperty("alpha1", VariantProperty(lamval_f))
soft_cljff02.setProperty("alpha1", VariantProperty(1 - lamval_f))
soft_cljff01.setProperty("coulombPower", VariantProperty(0))
soft_cljff01.setProperty("shiftDelta", VariantProperty(1.1))
soft_cljff02.setProperty("coulombPower", VariantProperty(0))
soft_cljff02.setProperty("shiftDelta", VariantProperty(1.1))
sys = System()
sys.add(cljff01)
sys.add(cljff02)
sys.add(soft_cljff01)
sys.add(soft_cljff02)
sys.add(ref)
sys.add(group_a)
sys.add(group_b)
sys.setComponent(lam, lamval)
sys.setComponent(lam_f, lamval_f)
sys.setComponent(sys.totalComponent(), nrg)
sys.setComponent(Symbol("E_{total_f}"), nrg_f)
sys.setComponent(Symbol("dE"), de)
sys.setComponent(Symbol("E_soft_{total}"), soft_nrg)
sys.setComponent(Symbol("E_soft_{total_f}"), soft_nrg_f)
sys.setComponent(Symbol("dE_soft"), de_soft)
nrgmon = FreeEnergyMonitor(ref, group_a, group_b)
soft_nrgmon = FreeEnergyMonitor(ref, group_a, group_b)
soft_nrgmon.setCoulombPower(0)
soft_nrgmon.setShiftDelta(1.1)
sys.add("nrgmon", nrgmon)
sys.add("soft_nrgmon", soft_nrgmon)
sys.collectStats()
nrgmon = sys[MonitorName("nrgmon")]
dg = nrgmon.freeEnergies()[0].average()
soft_nrgmon = sys[MonitorName("soft_nrgmon")]
soft_dg = soft_nrgmon.freeEnergies()[0].average()
sys_dg = sys.energy(Symbol("dE")).value()
sys_soft_dg = sys.energy(Symbol("dE_soft")).value()
assert_almost_equal(dg, sys_dg, 5)
assert_almost_equal(soft_dg, sys_soft_dg, 5)
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))
protoms.addParameterFile("test/io/oscillators.ff")
oscillator = protoms.parameterise(oscillator, ProtoMS.SOLUTE)
print("...parameterisation complete!")
internalff = InternalFF("InternalFF")
internalff.add(oscillator)
system = System()
system.add(internalff)
lam = Symbol("lambda")
system.setComponent(lam, 0.01)
system.setComponent(system.totalComponent(),
lam * internalff.components().total())
system.add("average energy", MonitorComponent(system.totalComponent()))
lambda_values = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
replicas = Replicas(system, len(lambda_values))
replicas.setLambdaComponent(lam)
for i in range(0, len(lambda_values)):
replicas.setLambdaValue(i, lambda_values[i])
# Add the protein
cljff.add(protein)
# Now also add a forcefield to calculate the intramolecular
# bond, angle and dihedral energy of the protein
intraff = InternalFF("intraff")
# Add the protein
intraff.add(protein)
# Add the forcefields to the system
system.add(cljff)
system.add(intraff)
# Set the expression used to calculate the total energy
# of the system
system.setComponent( system.totalComponent(),
cljff.components().total() +
intraff.components().total() )
# Tell the system about the periodic box
system.setProperty("space", space)
system.add( SpaceWrapper(Vector(0), protein) )
system.applyConstraints()
# Save a binary representation of the system
# to the file "protein.s3"
import Sire.Stream
Sire.Stream.save( system, "protein.s3" )
protoms.addParameterFile( "test/io/oscillators.ff" )
oscillator = protoms.parameterise(oscillator, ProtoMS.SOLUTE)
print("...parameterisation complete!")
internalff = InternalFF("InternalFF")
internalff.add( oscillator )
system = System()
system.add( internalff )
lam = Symbol("lambda")
system.setComponent(lam, 0.01)
system.setComponent(system.totalComponent(), lam * internalff.components().total())
system.add( "average energy", MonitorComponent(system.totalComponent()) )
lambda_values = [ 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 ]
replicas = Replicas(system, len(lambda_values))
replicas.setLambdaComponent(lam)
for i in range(0,len(lambda_values)):
replicas.setLambdaValue(i, lambda_values[i])
zmatmove = ZMatMove( internalff.groups()[0] )
# Sire performs simulations on simulation System objects.
# A System groups together all of the molecules, forcefields etc.
# into a single unit
system = System()
system.add(cljff)
# Here we create the equation used to calculate the total energy of the
# system. We define a symbol, lambda, which we use here to scale up and
# down the coulomb component of cljff
lam = Symbol("lambda")
total_nrg = cljff.components().lj() + lam * cljff.components().coulomb()
# Here we tell the system to use our equation to calculate the total
# energy, and we set the value of lambda to 0.5
system.setComponent(system.totalComponent(), total_nrg)
system.setConstant(lam, 0.5)
# Now we create a MoleculeGroup that groups together all of the
# molecules to be moved
mobile_mols = MoleculeGroup("mobile_molecules")
mobile_mols.add(first_water)
mobile_mols.add(second_water)
# We add the molecule group to the system
system.add(mobile_mols)
# We create a periodic boundaries space, and give it to the system
space = PeriodicBox(Vector(5, 5, 5))
system.setProperty("space", space)
