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
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]
crd3 = crds_bf_min[i[2]-1]
crd4 = crds_bf_min[i[3]-1]
dih = calc_dih(crd1, crd2, crd3, crd4)
val_bf_min.append(('dih', dih))
print("Bond, angle and dihedral before minimization...")
print(val_bf_min)
#-----------------------------------------------------------------------------#
#Get the Amber mask of the metal center complex and print it into ptraj.in file
#-----------------------------------------------------------------------------#
#Print the parmed input file, add new LJ types to the bonded atoms
maskns = []
for i in smcids:
maskn = str(mol.atoms[i].resid) + '@' + mol.atoms[i].atname
maskns.append(maskn)
def get_dih_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, nat4, n1, n2,
scalef):
crd1 = crds[3 * nat1 - 3:3 * nat1]
crd2 = crds[3 * nat2 - 3:3 * nat2]
crd3 = crds[3 * nat3 - 3:3 * nat3]
crd4 = crds[3 * nat4 - 3:3 * nat4]
dihval = calc_dih(crd1, crd2, crd3, crd4)
dis12 = calc_bond(crd1, crd2) #unit is bohr
dis23 = calc_bond(crd2, crd3) #unit is bohr
dis34 = calc_bond(crd3, crd4) #unit is bohr
#get the unit vector
vec12 = array(crd2) - array(crd1) #vec12 is vec2 - vec1
vec21 = -vec12
vec23 = array(crd3) - array(crd2)
vec32 = -vec23
vec34 = array(crd4) - array(crd3)
vec43 = -vec34
vec12 = array([i / dis12 for i in vec12])
vec21 = array([i / dis12 for i in vec21])
vec23 = array([i / dis23 for i in vec23])
vec32 = array([i / dis23 for i in vec32])
vec34 = array([i / dis34 for i in vec34])
vec43 = array([i / dis34 for i in vec43])
#get the normalized vector
vecUNABCp = cross(vec32, vec12)
vecUNABC = array([i / norm(vecUNABCp) for i in vecUNABCp])
vecUNBCDp = cross(vec43, vec23)
vecUNBCD = array([i / norm(vecUNBCDp) for i in vecUNBCDp])
afcmatrix12 = array([[float(0) for x in range(3)] for x in range(3)])
afcmatrix43 = array([[float(0) for x in range(3)] for x in range(3)])
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3 * (nat1 - 1) + i][3 *
(nat2 - 1) + j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix43[i][j] = -fcmatrix[3 * (nat4 - 1) + i][3 *
(nat3 - 1) + j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval43, eigvector43 = eig(afcmatrix43)
contri12 = 0.0
contri34 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:, i]
ev43 = eigvector43[:, i]
contri12 = contri12 + eigval12[i] * abs(dot(vecUNABC, ev12))
contri34 = contri34 + eigval43[i] * abs(dot(vecUNBCD, ev43))
contri12 = contri12 * (norm(cross(vec12, vec23))**2)
contri34 = contri34 * (norm(cross(vec23, vec34))**2)
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri34 = 1.0 / (contri34 * dis34 * dis34)
fcfinal1 = (
1.0 /
(contri12 + contri34)) * H_TO_KCAL_MOL * 0.5 #/ (math.degrees(1.0)**2)
fcfinal = fcfinal1 * (math.radians(
180.0 / float(n2)))**2 / (float(n1) * float(n2))
fcfinal = fcfinal * scalef * scalef
return dihval, fcfinal1, fcfinal
def get_dih_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, nat4, n1, n2, scalef):
crd1 = crds[3*nat1-3:3*nat1]
crd2 = crds[3*nat2-3:3*nat2]
crd3 = crds[3*nat3-3:3*nat3]
crd4 = crds[3*nat4-3:3*nat4]
dihval = calc_dih(crd1, crd2, crd3, crd4)
dis12 = calc_bond(crd1, crd2) #unit is bohr
dis23 = calc_bond(crd2, crd3) #unit is bohr
dis34 = calc_bond(crd3, crd4) #unit is bohr
#get the unit vector
vec12 = array(crd2) - array(crd1) #vec12 is vec2 - vec1
vec21 = - vec12
vec23 = array(crd3) - array(crd2)
vec32 = - vec23
vec34 = array(crd4) - array(crd3)
vec43 = - vec34
vec12 = array([i/dis12 for i in vec12])
vec21 = array([i/dis12 for i in vec21])
vec23 = array([i/dis23 for i in vec23])
vec32 = array([i/dis23 for i in vec32])
vec34 = array([i/dis34 for i in vec34])
vec43 = array([i/dis34 for i in vec43])
#get the normalized vector
vecUNABCp = cross(vec32, vec12)
vecUNABC = array([i/norm(vecUNABCp) for i in vecUNABCp])
vecUNBCDp = cross(vec43, vec23)
vecUNBCD = array([i/norm(vecUNBCDp) for i in vecUNBCDp])
afcmatrix12 = array([[float(0) for x in range(3)] for x in range(3)])
afcmatrix43 = array([[float(0) for x in range(3)] for x in range(3)])
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3*(nat1-1)+i][3*(nat2-1)+j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix43[i][j] = -fcmatrix[3*(nat4-1)+i][3*(nat3-1)+j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval43, eigvector43 = eig(afcmatrix43)
contri12 = 0.0
contri34 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:,i]
ev43 = eigvector43[:,i]
contri12 = contri12 + eigval12[i] * abs(dot(vecUNABC, ev12))
contri34 = contri34 + eigval43[i] * abs(dot(vecUNBCD, ev43))
contri12 = contri12 * (norm(cross(vec12, vec23)) ** 2)
contri34 = contri34 * (norm(cross(vec23, vec34)) ** 2)
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri34 = 1.0 / (contri34 * dis34 * dis34)
fcfinal1 = (1.0 / (contri12 + contri34)) * H_TO_KCAL_MOL * 0.5 #/ (math.degrees(1.0)**2)
fcfinal = fcfinal1 * (math.radians(180.0/float(n2))) **2 / (float(n1) * float(n2))
fcfinal = fcfinal * scalef * scalef
return dihval, fcfinal1, fcfinal
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
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]
crd3 = crds_bf_min[i[2] - 1]
crd4 = crds_bf_min[i[3] - 1]
dih = calc_dih(crd1, crd2, crd3, crd4)
val_bf_min.append(('dih', dih))
#print("Bond, angle and dihedral before minimization...")
#print(val_bf_min)
#-----------------------------------------------------------------------------#
#Get the Amber mask of the metal center complex and print it into ptraj.in file
#-----------------------------------------------------------------------------#
#Print the parmed input file, add new LJ types to the bonded atoms
maskns = []
for i in smcids:
maskn = str(mol.atoms[i].resid) + '@' + mol.atoms[i].atname
maskns.append(maskn)
