def read_amber_prm(pfile, cfile):
prmtop = AmberParm(pfile)
crds = read_rstf(cfile)
atids = list(range(1, len(prmtop.parm_data['ATOM_NAME']) + 1))
resids = list(range(1, len(prmtop.parm_data['RESIDUE_LABEL']) + 1))
if len(prmtop.parm_data['ATOM_NAME']) != len(crds):
raise ReadError('The toplogy and coordinates file are not \
consistent in the atom numbers.')
residues = {}
atoms = {}
for i in range(0, len(prmtop.parm_data['RESIDUE_LABEL'])):
resid = i + 1
resname = prmtop.parm_data['RESIDUE_LABEL'][i]
if i < len(prmtop.parm_data['RESIDUE_LABEL']) - 1:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
prmtop.parm_data['RESIDUE_POINTER'][i+1]))
else:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
len(prmtop.parm_data['ATOM_NAME'])+1))
residues[resid] = Residue(resid, resname, resconter)
for j in resconter:
gtype = 'ATOM'
atid = j
atname = prmtop.parm_data['ATOM_NAME'][j - 1]
element = prmtop.parm_data['ATOMIC_NUMBER'][j - 1]
atomtype = prmtop.parm_data['AMBER_ATOM_TYPE'][j - 1]
crd = crds[j - 1]
charge = prmtop.parm_data['CHARGE'][j - 1]
try:
element = AtnumRev[element]
except:
print(resname, atname, atomtype)
element = 'X'
atoms[j] = Atom(gtype, atid, atname, element, atomtype, crd, charge, \
resid, resname)
mol = Molecule(atoms, residues)
return prmtop, mol, atids, resids
def read_amber_prm(pfile, cfile):
prmtop = AmberParm(pfile)
crds = read_rstf(cfile)
atids = list(range(1, len(prmtop.parm_data['ATOM_NAME'])+1))
resids = list(range(1, len(prmtop.parm_data['RESIDUE_LABEL'])+1))
if len(prmtop.parm_data['ATOM_NAME']) != len(crds):
raise ReadError('The toplogy and coordinates file are not \
consistent in the atom numbers.')
residues = {}
atoms = {}
for i in range(0, len(prmtop.parm_data['RESIDUE_LABEL'])):
resid = i + 1
resname = prmtop.parm_data['RESIDUE_LABEL'][i]
if i < len(prmtop.parm_data['RESIDUE_LABEL'])-1:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
prmtop.parm_data['RESIDUE_POINTER'][i+1]))
else:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
len(prmtop.parm_data['ATOM_NAME'])+1))
residues[resid] = Residue(resid, resname, resconter)
for j in resconter:
gtype = 'ATOM'
atid = j
atname = prmtop.parm_data['ATOM_NAME'][j-1]
element = prmtop.parm_data['ATOMIC_NUMBER'][j-1]
atomtype = prmtop.parm_data['AMBER_ATOM_TYPE'][j-1]
crd = crds[j-1]
charge = prmtop.parm_data['CHARGE'][j-1]
try:
element = AtnumRev[element]
except:
print(resname, atname, atomtype)
element = 'X'
atoms[j] = Atom(gtype, atid, atname, element, atomtype, crd, charge, \
resid, resname)
mol = Molecule(atoms, residues)
return prmtop, mol, atids, resids
def get_rmsd(initparas):
global idxs, mcresids2, atompairs
#Modify the C4 terms in the prmtop file
for i in range(0, len(idxs)):
prmtop.parm_data['LENNARD_JONES_CCOEF'][idxs[i]] = initparas[i]
#Overwrite the prmtop file
prmtop.write_parm('OptC4.top')
#Perform the OpenMM optimization
#Use AmberParm function to transfer the topology and
#coordinate file to the object OpenMM can use
Ambermol = AmberParm('OptC4.top', options.cfile)
# Create the OpenMM system
print('Creating OpenMM System')
if options.simupha == 'gas':
system = Ambermol.createSystem(nonbondedMethod=app.NoCutoff)
elif options.simupha == 'liquid':
system = Ambermol.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8.0*u.angstroms,
constraints=app.HBonds,)
#Add restraints
force = mm.CustomExternalForce("k*((x-x0)^2+(y-y0)^2+(z-z0)^2)")
force.addGlobalParameter("k", 200.0)
force.addPerParticleParameter("x0")
force.addPerParticleParameter("y0")
force.addPerParticleParameter("z0")
#for i in range(0, len(Ambermol.atoms)):
for i, atom_crd in enumerate(Ambermol.positions):
#if (Ambermol.atoms[i].residue.number+1 not in mcresids2) and \
if (i+1 not in mcresids2) and \
(Ambermol.atoms[i].residue.name not in ['WAT', 'HOH']) and \
(Ambermol.atoms[i].name in ['CA', 'C', 'N']):
force.addParticle(i, atom_crd.value_in_unit(u.nanometers))
system.addForce(force)
# Create the integrator to do Langevin dynamics
# Temperature of heat bath, Friction coefficient, Time step
integrator = mm.LangevinIntegrator(300*u.kelvin, 1.0/u.picoseconds,
1.0*u.femtoseconds,)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not
# specify the platform to use the default (fastest) platform
# Create the Simulation object
if options.platf == 'ref':
platform = mm.Platform.getPlatformByName('Reference')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cpu':
platform = mm.Platform.getPlatformByName('CPU')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cuda':
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
elif options.platf == 'opencl':
platform = mm.Platform.getPlatformByName('OpenCL')
prop = dict(CudaPrecision='mixed')
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
# Set the particle positions
sim.context.setPositions(Ambermol.positions)
# Output the rst file
restrt = RestartReporter(options.rfile, 100, write_velocities=False)
sim.reporters.append(restrt)
# Minimize the energy
print('Minimizing energy ' + str(options.maxsteps) + ' steps.')
sim.minimizeEnergy(maxIterations=options.maxsteps)
# Overwrite the final file
state = sim.context.getState(getPositions=True, enforcePeriodicBox=True)
restrt.report(sim, state)
val_aft_min = []
crds_aft_min = read_rstf(options.rfile)
for i in atompairs:
if len(i) == 2:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
bond = calc_bond(crd1, crd2)
val_aft_min.append(('bond', bond))
elif len(i) == 3:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
crd3 = crds_aft_min[i[2]-1]
angle = calc_angle(crd1, crd2, crd3)
val_aft_min.append(('angle', angle))
elif len(i) == 4:
crd1 = crds_aft_min[i[0]-1]
crd2 = crds_aft_min[i[1]-1]
crd3 = crds_aft_min[i[2]-1]
crd4 = crds_aft_min[i[3]-1]
dih = calc_dih(crd1, crd2, crd3, crd4)
val_aft_min.append(('dih', dih))
valdiffs = []
for i in range(0, len(atompairs)):
if val_bf_min[i][0] == 'bond':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 100.0
elif val_bf_min[i][0] == 'angle':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 2.0
elif val_bf_min[i][0] == 'dih':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1])
if (360.0 - valdiff < valdiff):
valdiff = 360.0 - valdiff
valdiffs.append(valdiff)
fnldiff = numpy.sum(valdiffs)
print(fnldiff)
return fnldiff
mcresids2.sort()
print('Residues in the metal site: ', mcresids2)
mcids = [] #Metal site atom IDs
if options.model == 1: #Small model
mcids = smcids
elif options.model == 2: #Big model
for i in mcresids:
for j in mol.residues[i].resconter:
if mol.atoms[j].element != 'H':
mcids.append(j)
#Calculate the distances between metal ion and ligating atoms
val_bf_min = []
crds_bf_min = read_rstf(options.cfile)
for i in atompairs:
if len(i) == 2:
crd1 = crds_bf_min[i[0]-1]
crd2 = crds_bf_min[i[1]-1]
bond = calc_bond(crd1, crd2)
val_bf_min.append(('bond', bond))
elif len(i) == 3:
crd1 = crds_bf_min[i[0]-1]
crd2 = crds_bf_min[i[1]-1]
crd3 = crds_bf_min[i[2]-1]
angle = calc_angle(crd1, crd2, crd3)
val_bf_min.append(('angle', angle))
elif len(i) == 4:
crd1 = crds_bf_min[i[0]-1]
crd2 = crds_bf_min[i[1]-1]
def get_rmsd(initparas):
global idxs, mcresids2, atompairs
#Modify the C4 terms in the prmtop file
for i in range(0, len(idxs)):
prmtop.parm_data['LENNARD_JONES_CCOEF'][idxs[i]] = initparas[i]
#Overwrite the prmtop file
prmtop.write_parm('OptC4.top')
#Perform the OpenMM optimization
#Use AmberParm function to transfer the topology and
#coordinate file to the object OpenMM can use
Ambermol = AmberParm('OptC4.top', options.cfile)
# Create the OpenMM system
print('Creating OpenMM System')
if options.simupha == 'gas':
system = Ambermol.createSystem(nonbondedMethod=app.NoCutoff)
elif options.simupha == 'liquid':
system = Ambermol.createSystem(
nonbondedMethod=app.PME,
nonbondedCutoff=8.0 * u.angstroms,
constraints=app.HBonds,
)
#Add restraints
force = mm.CustomExternalForce("k*((x-x0)^2+(y-y0)^2+(z-z0)^2)")
force.addGlobalParameter("k", 200.0)
force.addPerParticleParameter("x0")
force.addPerParticleParameter("y0")
force.addPerParticleParameter("z0")
#for i in range(0, len(Ambermol.atoms)):
for i, atom_crd in enumerate(Ambermol.positions):
#if (Ambermol.atoms[i].residue.number+1 not in mcresids2) and \
if (i+1 not in mcresids2) and \
(Ambermol.atoms[i].residue.name not in ['WAT', 'HOH']) and \
(Ambermol.atoms[i].name in ['CA', 'C', 'N']):
force.addParticle(i, atom_crd.value_in_unit(u.nanometers))
system.addForce(force)
# Create the integrator to do Langevin dynamics
# Temperature of heat bath, Friction coefficient, Time step
integrator = mm.LangevinIntegrator(
300 * u.kelvin,
1.0 / u.picoseconds,
1.0 * u.femtoseconds,
)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not
# specify the platform to use the default (fastest) platform
# Create the Simulation object
if options.platf == 'ref':
platform = mm.Platform.getPlatformByName('Reference')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cpu':
platform = mm.Platform.getPlatformByName('CPU')
sim = app.Simulation(Ambermol.topology, system, integrator, platform)
elif options.platf == 'cuda':
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision=options.presn)
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
elif options.platf == 'opencl':
platform = mm.Platform.getPlatformByName('OpenCL')
prop = dict(OpenCLPrecision=options.presn)
sim = app.Simulation(Ambermol.topology, system, integrator, platform,
prop)
# Set the particle positions
sim.context.setPositions(Ambermol.positions)
# Output the rst file
restrt = RestartReporter(options.rfile, 100, write_velocities=False)
sim.reporters.append(restrt)
# Minimize the energy
print('Minimizing energy ' + str(options.maxsteps) + ' steps.')
sim.minimizeEnergy(maxIterations=options.maxsteps)
# Overwrite the final file
state = sim.context.getState(getPositions=True, enforcePeriodicBox=True)
restrt.report(sim, state)
val_aft_min = []
crds_aft_min = read_rstf(options.rfile)
for i in atompairs:
if len(i) == 2:
crd1 = crds_aft_min[i[0] - 1]
crd2 = crds_aft_min[i[1] - 1]
bond = calc_bond(crd1, crd2)
val_aft_min.append(('bond', bond))
elif len(i) == 3:
crd1 = crds_aft_min[i[0] - 1]
crd2 = crds_aft_min[i[1] - 1]
crd3 = crds_aft_min[i[2] - 1]
angle = calc_angle(crd1, crd2, crd3)
val_aft_min.append(('angle', angle))
elif len(i) == 4:
crd1 = crds_aft_min[i[0] - 1]
crd2 = crds_aft_min[i[1] - 1]
crd3 = crds_aft_min[i[2] - 1]
crd4 = crds_aft_min[i[3] - 1]
dih = calc_dih(crd1, crd2, crd3, crd4)
val_aft_min.append(('dih', dih))
valdiffs = []
for i in range(0, len(atompairs)):
if val_bf_min[i][0] == 'bond':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 100.0
elif val_bf_min[i][0] == 'angle':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1]) * 1.0 / 2.0
elif val_bf_min[i][0] == 'dih':
valdiff = abs(val_aft_min[i][1] - val_bf_min[i][1])
if (360.0 - valdiff < valdiff):
valdiff = 360.0 - valdiff
valdiffs.append(valdiff)
fnldiff = numpy.sum(valdiffs)
print(fnldiff)
return fnldiff
mcresids2.sort()
print('Residues in the metal site: ', mcresids2)
mcids = [] #Metal site atom IDs
if options.model == 1: #Small model
mcids = smcids
elif options.model == 2: #Big model
for i in mcresids:
for j in mol.residues[i].resconter:
if mol.atoms[j].element != 'H':
mcids.append(j)
#Calculate the distances between metal ion and ligating atoms
val_bf_min = []
crds_bf_min = read_rstf(options.cfile)
for i in atompairs:
if len(i) == 2:
crd1 = crds_bf_min[i[0] - 1]
crd2 = crds_bf_min[i[1] - 1]
bond = calc_bond(crd1, crd2)
val_bf_min.append(('bond', bond))
elif len(i) == 3:
crd1 = crds_bf_min[i[0] - 1]
crd2 = crds_bf_min[i[1] - 1]
crd3 = crds_bf_min[i[2] - 1]
angle = calc_angle(crd1, crd2, crd3)
val_bf_min.append(('angle', angle))
elif len(i) == 4:
crd1 = crds_bf_min[i[0] - 1]
crd2 = crds_bf_min[i[1] - 1]