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
def get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg):
#get the angle value
crd1 = crds[3 * nat1 - 3:3 * nat1]
crd2 = crds[3 * nat2 - 3:3 * nat2]
crd3 = crds[3 * nat3 - 3:3 * nat3]
dis12 = calc_bond(crd1, crd2) #unit is bohr
dis32 = calc_bond(crd3, crd2) #unit is bohr
#get the unit vector
vec12 = array(crd2) - array(crd1) #vec12 is vec2 - vec1
vec32 = array(crd2) - array(crd3)
vec12 = array([i / dis12 for i in vec12])
vec32 = array([i / dis32 for i in vec32])
angval = calc_angle(crd1, crd2, crd3)
#get the normalized vector
vecUNp = cross(vec32, vec12)
vecUN = array([i / norm(vecUNp) for i in vecUNp]) #vecUN is the vector
#perpendicular to the plance of ABC
vecPA = cross(vecUN, vec12)
vecPC = cross(vec32, vecUN)
afcmatrix12 = array([[float(0) for x in range(3)] for x in range(3)])
afcmatrix32 = array([[float(0) for x in range(3)] for x in range(3)])
#1. First way to chose the matrix----------------------------------
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):
afcmatrix32[i][j] = -fcmatrix[3 * (nat3 - 1) + i][3 *
(nat2 - 1) + j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:, i]
ev32 = eigvector32[:, i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal1 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
if angavg == 1:
#2. Second way to chose the matrix----------------------------------
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3 *
(nat2 - 1) + i][3 *
(nat1 - 1) + j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix32[i][j] = -fcmatrix[3 *
(nat3 - 1) + i][3 *
(nat2 - 1) + j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:, i]
ev32 = eigvector32[:, i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal2 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
#Hatree to kcal/mol
#Times 0.5 factor since AMBER use k(r-r0)^2 but not 1/2*k*(r-r0)^2
#3. Third way to chose the matrix----------------------------------
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):
afcmatrix32[i][j] = -fcmatrix[3 *
(nat2 - 1) + i][3 *
(nat3 - 1) + j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:, i]
ev32 = eigvector32[:, i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal3 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
#4. Fourth way to chose the matrix----------------------------------
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3 *
(nat2 - 1) + i][3 *
(nat1 - 1) + j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix32[i][j] = -fcmatrix[3 *
(nat2 - 1) + i][3 *
(nat3 - 1) + j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:, i]
ev32 = eigvector32[:, i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal4 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
fcfinal = average([fcfinal1, fcfinal2, fcfinal3, fcfinal4])
stdv = std([fcfinal1, fcfinal2, fcfinal3, fcfinal4])
fcfinal = fcfinal * scalef * scalef
stdv = stdv * scalef * scalef
return angval, fcfinal, stdv
elif angavg == 0:
fcfinal = fcfinal1 * scalef * scalef
return angval, fcfinal
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]
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
#-----------------------------------------------------------------------------#
def gene_by_empirical_way(smpdbf, ionids, stfpf, pref, finf):
print("******************************************************************")
print("* *")
print("*===========Using the empirical way to solve the problem=========*")
print("* *")
print("******************************************************************")
#Read from small pdb
mol, atids, resids = get_atominfo_fpdb(smpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print("=======================Generate the bond parameters===============")
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
if bondtyp == misbond or bondtyp[::-1] == misbond:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
dis = calc_bond(crd1, crd2)
dis = round(dis, 4)
bondlen.append(dis)
#get the atom number
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmts = [elmt1, elmt2]
elmts = sorted(elmts)
fcfinal = fcfit_ep_bond(dis, elmts)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print("=======================Generate the angle parameters==============")
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
crd3 = mol.atoms[at3].crd
angval = calc_angle(crd1, crd2, crd3)
angvals.append(angval)
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmt3 = mol.atoms[at3].element
elmts = [elmt1, elmt2, elmt3]
fcfinal = fcfit_ep_angle(elmts)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'empirical')
def get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg):
#get the angle value
crd1 = crds[3*nat1-3:3*nat1]
crd2 = crds[3*nat2-3:3*nat2]
crd3 = crds[3*nat3-3:3*nat3]
dis12 = calc_bond(crd1, crd2) #unit is bohr
dis32 = calc_bond(crd3, crd2) #unit is bohr
#get the unit vector
vec12 = array(crd2) - array(crd1) #vec12 is vec2 - vec1
vec32 = array(crd2) - array(crd3)
vec12 = array([i/dis12 for i in vec12])
vec32 = array([i/dis32 for i in vec32])
angval = calc_angle(crd1, crd2, crd3)
#get the normalized vector
vecUNp = cross(vec32, vec12)
vecUN = array([i/norm(vecUNp) for i in vecUNp]) #vecUN is the vector
#perpendicular to the plance of ABC
vecPA = cross(vecUN, vec12)
vecPC = cross(vec32, vecUN)
afcmatrix12 = array([[float(0) for x in range(3)] for x in range(3)])
afcmatrix32 = array([[float(0) for x in range(3)] for x in range(3)])
#1. First way to chose the matrix----------------------------------
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):
afcmatrix32[i][j] = -fcmatrix[3*(nat3-1)+i][3*(nat2-1)+j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:,i]
ev32 = eigvector32[:,i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal1 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
if angavg == 1:
#2. Second way to chose the matrix----------------------------------
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3*(nat2-1)+i][3*(nat1-1)+j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix32[i][j] = -fcmatrix[3*(nat3-1)+i][3*(nat2-1)+j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:,i]
ev32 = eigvector32[:,i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal2 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
#Hatree to kcal/mol
#Times 0.5 factor since AMBER use k(r-r0)^2 but not 1/2*k*(r-r0)^2
#3. Third way to chose the matrix----------------------------------
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):
afcmatrix32[i][j] = -fcmatrix[3*(nat2-1)+i][3*(nat3-1)+j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:,i]
ev32 = eigvector32[:,i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal3 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
#4. Fourth way to chose the matrix----------------------------------
for i in range(0, 3):
for j in range(0, 3):
afcmatrix12[i][j] = -fcmatrix[3*(nat2-1)+i][3*(nat1-1)+j]
for i in range(0, 3):
for j in range(0, 3):
afcmatrix32[i][j] = -fcmatrix[3*(nat2-1)+i][3*(nat3-1)+j]
eigval12, eigvector12 = eig(afcmatrix12)
eigval32, eigvector32 = eig(afcmatrix32)
contri12 = 0.0
contri32 = 0.0
for i in range(0, 3):
ev12 = eigvector12[:,i]
ev32 = eigvector32[:,i]
contri12 = contri12 + eigval12[i] * abs(dot(vecPA, ev12))
contri32 = contri32 + eigval32[i] * abs(dot(vecPC, ev32))
contri12 = 1.0 / (contri12 * dis12 * dis12)
contri32 = 1.0 / (contri32 * dis32 * dis32)
fcfinal4 = (1.0 / (contri12 + contri32)) * H_TO_KCAL_MOL * 0.5
fcfinal = average([fcfinal1, fcfinal2, fcfinal3, fcfinal4])
stdv = std([fcfinal1, fcfinal2, fcfinal3, fcfinal4])
fcfinal = fcfinal * scalef * scalef
stdv = stdv * scalef * scalef
return angval, fcfinal, stdv
elif angavg == 0:
fcfinal = fcfinal1 * scalef * scalef
return angval, fcfinal
def gene_by_empirical_way(smpdbf, ionids, stfpf, pref, finf):
print("******************************************************************")
print("* *")
print("*===========Using the empirical way to solve the problem=========*")
print("* *")
print("******************************************************************")
#Read from small pdb
mol, atids, resids = get_atominfo_fpdb(smpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print("=======================Generate the bond parameters===============")
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
if bondtyp == misbond or bondtyp[::-1] == misbond:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
dis = calc_bond(crd1, crd2)
dis = round(dis, 4)
bondlen.append(dis)
#get the atom number
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmts = [elmt1, elmt2]
elmts = sorted(elmts)
fcfinal = fcfit_ep_bond(dis, elmts)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print("=======================Generate the angle parameters==============")
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
crd3 = mol.atoms[at3].crd
angval = calc_angle(crd1, crd2, crd3)
angvals.append(angval)
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmt3 = mol.atoms[at3].element
elmts = [elmt1, elmt2, elmt3]
fcfinal = fcfit_ep_angle(elmts)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'empirical')
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
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]
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
#-----------------------------------------------------------------------------#
