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Commit 00e88bff authored by huangj's avatar huangj
Browse files

Update the python api for parsing CHARMM par/top/psf files.

parent 7a8c03dd
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Showing with 268 additions and 16 deletions
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 00e88bff
......@@ -114,6 +114,7 @@ class CharmmParameterSet(object):
self.improper_types = dict()
self.cmap_types = dict()
self.nbfix_types = dict()
self.nbthole_types = dict()
self.parametersets = []
# Load all of the files
......@@ -261,6 +262,9 @@ class CharmmParameterSet(object):
if line.startswith('NBFIX'):
section = 'NBFIX'
continue
if line.startswith('THOLE'):
section = 'NBTHOLE'
continue
if line.startswith('HBOND'):
section = None
continue
......@@ -493,6 +497,21 @@ class CharmmParameterSet(object):
except IndexError:
raise CharmmFileError('Could not parse NBFIX terms.')
self.nbfix_types[(min(at1, at2), max(at1, at2))] = (emin, rmin)
# Here parse the possible nbthole section
if section == 'NBTHOLE':
words = line.split()
try:
at1 = words[0]
at2 = words[1]
nbt = abs(conv(words[2], float, 'NBTHOLE a'))
try:
self.atom_types_str[at1].add_nbthole(at2, nbt)
self.atom_types_str[at2].add_nbthole(at1, nbt)
except KeyError:
pass
except IndexError:
raise CharmmFileError('Could not parse NBTHOLE terms.')
self.nbthole_types[(min(at1, at2), max(at1, at2))] = (nbt)
# If there were any CMAP terms stored in the parameter set, the last one
# defined will not have been added to the set. Add it now.
if current_cmap is not None:
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 00e88bff
......@@ -57,7 +57,7 @@ from simtk.openmm.app.internal.charmm.exceptions import (
import warnings
TINY = 1e-8
WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC')
WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC', 'SWM4', 'SWM6')
if sys.version_info >= (3, 0):
xrange = range
......@@ -236,19 +236,31 @@ class CharmmPsfFile(object):
atom = residue_list.add_atom(system, resid, resname, name,
attype, charge, mass, inscode, props)
atom_list.append(atom)
if IsDrudePSF:
alpha = conv(words[9], float, 'alpha')
thole = conv(words[10], float, 'thole')
drudeconsts_list.append([alpha, thole])
atom_list.assign_indexes()
atom_list.changed = False
# Now get the number of bonds
nbond = conv(psfsections['NBOND'][0], int, 'number of bonds')
holder = psfsections['NBOND'][1]
bond_list = TrackedList()
if IsDrudePSF:
drudepair_list = TrackedList()
if len(holder) != nbond * 2:
raise CharmmPSFError('Got %d indexes for %d bonds' %
(len(holder), nbond))
for i in range(nbond):
id1 = holder[2*i ] - 1
id2 = holder[2*i+1] - 1
bond_list.append(Bond(atom_list[id1], atom_list[id2]))
# ignore any bond pair involving Drude or lonepairs: possible using atom's prop
if (atom_list[id1].name[0]=='D' or atom_list[id2].name[0]=='D'):
drudepair_list.append([min(id1,id2), max(id1,id2)])
elif (atom_list[id1].name[0:2]=='LP' or atom_list[id2].name[0:2]=='LP' or atom_list[id1].name=='OM' or atom_list[id2].name=='OM'):
pass
else:
bond_list.append(Bond(atom_list[id1], atom_list[id2]))
bond_list.changed = False
# Now get the number of angles and the angle list
ntheta = conv(psfsections['NTHETA'][0], int, 'number of angles')
......@@ -349,12 +361,48 @@ class CharmmPsfFile(object):
if molecule_list != holder:
warnings.warn('Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmPSFWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplementedError('Cannot currently handle PSFs with lone '
'pairs defined in the NUMLP/NUMLPH '
'section.')
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
holder = psfsections['NUMLP NUMLPH'][1]
lonepair_list = TrackedList()
if numlp != 0 or numlph != 0:
lp_distance_list=[]
lp_angle_list=[]
lp_dihe_list=[]
for i in range(numlp):
lpline = holder[i].split()
if len(lpline)!=6 or lpline[0] != '3' or lpline[2] != 'F' or int(lpline[1]) != 4*i+1 :
raise CharmmPSFError('Lonepair format error')
else:
lp_distance_list.append(float(lpline[3]))
lp_angle_list.append(float(lpline[4]))
lp_dihe_list.append(float(lpline[5]))
for i in range(numlp):
lpline = holder[int(i/2)+numlp].split()
icolumn = (i%2) * 4
id1=int(lpline[icolumn]) -1
id2=int(lpline[icolumn+1])-1
id3=int(lpline[icolumn+2])-1
id4=int(lpline[icolumn+3])-1
lonepair_list.append([id1, id2, id3, id4, lp_distance_list[i], lp_angle_list[i], lp_dihe_list[i]])
# In Drude psf, here comes anisotropic section
if IsDrudePSF:
numaniso = psfsections['NUMANISO'][0]
holder = psfsections['NUMANISO'][1]
aniso_list = TrackedList()
if numaniso != 0:
k_list=[]
for i in range(numaniso):
lpline = holder[i].split()
k_list.append([float(lpline[0]),float(lpline[1]),float(lpline[2])])
for i in range(numaniso):
lpline = holder[int(i/2)+numaniso].split()
icolumn = (i%2) * 4
id1=int(lpline[icolumn]) -1
id2=int(lpline[icolumn+1])-1
id3=int(lpline[icolumn+2])-1
id4=int(lpline[icolumn+3])-1
aniso_list.append([id1, id2, id3, id4, k_list[i][0], k_list[i][1], k_list[i][2]])
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int, 'Number of cross-terms')
holder = psfsections['NCRTERM'][1]
......@@ -385,6 +433,11 @@ class CharmmPsfFile(object):
self.dihedral_list = dihedral_list
self.dihedral_parameter_list = TrackedList()
self.improper_list = improper_list
self.lonepair_list = lonepair_list
if IsDrudePSF:
self.drudeconsts_list = drudeconsts_list
self.drudepair_list = drudepair_list
self.aniso_list = aniso_list
self.cmap_list = cmap_list
self.donor_list = donor_list
self.acceptor_list = acceptor_list
......@@ -459,8 +512,8 @@ class CharmmPsfFile(object):
# blank line) as well as any sections that have 0 members.
line = psf.readline().strip()
data = []
if title == 'NATOM' or title == 'NTITLE':
# Store these two sections as strings (ATOM section we will parse
if title == 'NATOM' or title == 'NTITLE' or title == 'NUMLP NUMLPH' or title == 'NUMANISO':
# Store these four sections as strings (ATOM section we will parse
# later). The rest of the sections are integer pointers
while line:
data.append(line)
......@@ -787,7 +840,7 @@ class CharmmPsfFile(object):
u.kilojoule_per_mole)
ene_conv = dihe_frc_conv
# Create the system and determine if any of our atoms have NBFIX (and
# Create the system and determine if any of our atoms have NBFIX or NBTHOLE (and
# therefore requires a CustomNonbondedForce instead)
typenames = set()
system = mm.System()
......@@ -806,6 +859,17 @@ class CharmmPsfFile(object):
raise StopIteration
except StopIteration:
pass
has_nbthole_terms = False
try:
for i, typename in enumerate(typenames):
typ = params.atom_types_str[typename]
for j in range(i, len(typenames)):
if typenames[j] in typ.nbthole:
has_nbthole_terms = True
raise StopIteration
except StopIteration:
pass
# Set up the constraints
if verbose and (constraints is not None and not rigidWater):
print('Adding constraints...')
......@@ -832,6 +896,25 @@ class CharmmPsfFile(object):
bond.atom2.residue.resname in WATNAMES):
system.addConstraint(bond.atom1.idx, bond.atom2.idx,
bond.bond_type.req*length_conv)
# Add virtual sites
if verbose: print('Adding lonepairs...')
for lpsite in self.lonepair_list:
index=lpsite[0]
atom1=lpsite[1]
atom2=lpsite[2]
atom3=lpsite[3]
if lpsite[4] > 0 : #relative
r = lpsite[4] /10.0 # in nanometer
xweights = [-1.0, 0.0, 1.0]
elif lpsite[4] < 0: # bisector
r = lpsite[4] / (-10.0)
xweights = [-1.0, 0.5, 0.5]
theta = lpsite[5] * pi / 180.0
phi = (180.0 - lpsite[6]) * pi / 180.0
p = [r*cos(theta), r*sin(theta)*cos(phi), r*sin(theta)*sin(phi)]
p = [x if abs(x) > 1e-10 else 0 for x in p] # Avoid tiny numbers caused by roundoff error
system.setVirtualSite(index, mm.LocalCoordinatesSite(atom1, atom3, atom2, mm.Vec3(1.0, 0.0, 0.0), mm.Vec3(xweights[0],xweights[1],xweights[2]), mm.Vec3(0.0, -1.0, 1.0), mm.Vec3(p[0],p[1],p[2])))
# Add Bond forces
if verbose: print('Adding bonds...')
force = mm.HarmonicBondForce()
......@@ -1079,8 +1162,8 @@ class CharmmPsfFile(object):
if lj_idx_list[j] > 0: continue # already assigned
if atom2 is atom:
lj_idx_list[j] = num_lj_types
elif not atom.nbfix:
# Only non-NBFIXed atom types can be compressed
elif not atom.nbfix and not atom.nbthole:
# Only non-NBFIXed and non-NBTholed atom types can be compressed
ljtype2 = (atom2.rmin, atom2.epsilon)
if ljtype == ljtype2:
lj_idx_list[j] = num_lj_types
......@@ -1135,6 +1218,68 @@ class CharmmPsfFile(object):
for i in lj_idx_list:
cforce.addParticle((i - 1,)) # adjust for indexing from 0
# Add NBTHOLE terms
if IsDrudePSF and has_nbthole_terms:
nbt_idx_list = [0 for atom in self.atom_list]
nbt_alpha_list = [0 for atom in self.atom_list] # only save alpha for NBThole pairs
num_nbt_types = 0
nbt_type_list = []
nbt_set_list = []
for i, atom in enumerate(self.atom_list):
atom = atom.type
if not atom.nbthole: continue # get them as zero
if nbt_idx_list[i]: continue # already assigned
num_nbt_types += 1
nbt_idx_list[i] = num_nbt_types
nbt_idx_list[i+1] = num_nbt_types
nbt_alpha_list[i] = pow(-1*self.drudeconsts_list[i][0],-1./6.)
nbt_alpha_list[i+1] = pow(-1*self.drudeconsts_list[i][0],-1./6.)
nbt_type_list.append(atom)
nbt_set_list.append([i,i+1])
for j in range(i+1, len(self.atom_list)):
atom2 = self.atom_list[j].type
if nbt_idx_list[j] > 0: continue # already assigned
if atom2 is atom:
nbt_idx_list[j] = num_nbt_types
nbt_idx_list[j+1] = num_nbt_types
nbt_alpha_list[j] = pow(-1*self.drudeconsts_list[j][0],-1./6.)
nbt_alpha_list[j+1] = pow(-1*self.drudeconsts_list[j][0],-1./6.)
nbt_set_list[num_nbt_types-1].append(j)
nbt_set_list[num_nbt_types-1].append(j+1)
num_total_nbt=num_nbt_types+1 # use zero index for all the atoms with no nbthole
nbt_interset_list=[]
# need to get all other particles as an independent group, so in total num_nbt_types+1
coef = [0 for i in range(num_total_nbt*num_total_nbt)]
for i in range(num_nbt_types):
for j in range(num_nbt_types):
namej = nbt_type_list[j].name
nbt_value = nbt_type_list[i].nbthole.get(namej,0)
if abs(nbt_value)>TINY and i<j : nbt_interset_list.append([i+1,j+1])
coef[i+1+num_total_nbt*(j+1)]=nbt_value
nbtforce = mm.CustomNonbondedForce('-138.935456*charge1*charge2*(1.0+0.5*screen*r)*exp(-1.0*screen*r)/r; screen=coef(type1, type2) * alpha1*alpha2*10.0')
nbtforce.addTabulatedFunction('coef', mm.Discrete2DFunction(num_total_nbt, num_total_nbt, coef))
nbtforce.addPerParticleParameter('charge')
nbtforce.addPerParticleParameter('alpha')
nbtforce.addPerParticleParameter('type')
nbtforce.setForceGroup(self.NONBONDED_FORCE_GROUP)
# go through all the particles to set up per-particle parameters
for i in range(system.getNumParticles()):
c=force.getParticleParameters(i)
cc=c[0]/u.elementary_charge
aa=nbt_alpha_list[i]
ti=nbt_idx_list[i]
nbtforce.addParticle([cc,aa,ti])
# set interaction group
for a in nbt_interset_list:
ai=a[0]
aj=a[1]
nbtforce.addInteractionGroup(nbt_set_list[ai-1],nbt_set_list[aj-1])
nbtforce.setNonbondedMethod(nbtforce.CutoffPeriodic)
nbtforce.setCutoffDistance(0.5*u.nanometer)
nbtforce.setUseSwitchingFunction(False)
# now, add the actual force to the system
system.addForce(nbtforce)
# Add 1-4 interactions
excluded_atom_pairs = set() # save these pairs so we don't zero them out
sigma_scale = 2**(-1/6)
......@@ -1160,20 +1305,99 @@ class CharmmPsfFile(object):
)
# Add excluded atoms
# Drude and lonepairs will be excluded based on their parent atoms
parent_exclude_list=[]
for atom in self.atom_list:
parent_exclude_list.append([])
for lpsite in self.lonepair_list:
idx = lpsite[1]
idxa = lpsite[0]
parent_exclude_list[idx].append(idxa)
force.addException(idx, idxa, 0.0, 0.1, 0.0)
if IsDrudePSF:
for pair in self.drudepair_list:
idx = pair[0]
idxa = pair[1]
parent_exclude_list[idx].append(idxa)
force.addException(idx, idxa, 0.0, 0.1, 0.0)
# If lonepairs and Drude particles are bonded to the same parent atom, add exception
for excludeterm in parent_exclude_list:
if(len(excludeterm) >= 2):
for i in range(len(excludeterm)):
for j in range(i):
force.addException(excludeterm[j], excludeterm[i], 0.0, 0.1, 0.0)
# Exclude all bonds and angles, as well as the lonepair/Drude attached onto them
for atom in self.atom_list:
# Exclude all bonds and angles
for atom2 in atom.bond_partners:
if atom2.idx > atom.idx:
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
for atom2 in atom.angle_partners:
if atom2.idx > atom.idx:
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
for atom2 in atom.dihedral_partners:
if atom2.idx <= atom.idx: continue
if ((atom.idx, atom2.idx) in excluded_atom_pairs):
continue
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
system.addForce(force)
# Add Drude particles (Drude force)
if IsDrudePSF:
if verbose: print('Adding Drude force and Thole screening...')
drudeforce = mm.DrudeForce()
drudeforce.setForceGroup(7)
for pair in self.drudepair_list:
parentatom=pair[0]
drudeatom=pair[1]
p=[-1, -1, -1]
a11 = 0
a22 = 0
charge = self.atom_list[drudeatom].charge
polarizability = self.drudeconsts_list[parentatom][0]/(-1000.0)
for aniso in self.aniso_list: # not smart to do another loop, but the number of aniso is small anyway
if (parentatom==aniso[0]):
p[0]=aniso[1]
p[1]=aniso[2]
p[2]=aniso[3]
k11=aniso[4]
k22=aniso[5]
k33=aniso[6]
# solve out DrudeK, which should equal 500.0
a = k11+k22+3*k33
b = 2*k11*k22+4*k11*k33+4*k22*k33+6*k33*k33
c = 3*k33*(k11+k33)*(k22+k33)
DrudeK = (sqrt(b*b-4*a*c)-b)/2/a
a11=round(DrudeK/(k11+k33+DrudeK),5)
a22=round(DrudeK/(k22+k33+DrudeK),5)
drudeforce.addParticle(drudeatom, parentatom, p[0], p[1], p[2], charge, polarizability, a11, a22 )
system.addForce(drudeforce)
particleMap = {}
for i in range(drudeforce.getNumParticles()):
particleMap[drudeforce.getParticleParameters(i)[0]] = i
for bond in self.bond_list:
alpha1 = self.drudeconsts_list[bond.atom1.idx][0]
alpha2 = self.drudeconsts_list[bond.atom2.idx][0]
if abs(alpha1) > TINY and abs(alpha2) > TINY: # both are Drude parent atoms
thole1 = self.drudeconsts_list[bond.atom1.idx][1]
thole2 = self.drudeconsts_list[bond.atom2.idx][1]
drude1 = bond.atom1.idx + 1 # CHARMM psf has hard-coded rule that the Drude is next to its parent
drude2 = bond.atom2.idx + 1
drudeforce.addScreenedPair(particleMap[drude1], particleMap[drude2], thole1+thole2)
for ang in self.angle_list:
alpha1 = self.drudeconsts_list[ang.atom1.idx][0]
alpha2 = self.drudeconsts_list[ang.atom3.idx][0]
if abs(alpha1) > TINY and abs(alpha2) > TINY: # both are Drude parent atoms
thole1 = self.drudeconsts_list[ang.atom1.idx][1]
thole2 = self.drudeconsts_list[ang.atom3.idx][1]
drude1 = ang.atom1.idx + 1 # CHARMM psf has hard-coded rule that the Drude is next to its parent
drude2 = ang.atom3.idx + 1
drudeforce.addScreenedPair(particleMap[drude1], particleMap[drude2], thole1+thole2)
# If we needed a CustomNonbondedForce, map all of the exceptions from
# the NonbondedForce to the CustomNonbondedForce
if has_nbfix_terms:
......
wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py
View file @ 00e88bff
......@@ -100,6 +100,9 @@ class AtomType(object):
nbfix : dict
Dictionary that maps nbfix terms with other atom types. Dict entries
are (rmin, epsilon) -- precombined values for that particular atom pair
nbthole : dict
Dictionary that maps nbthole terms with other atom types. Dict entries
are the value of a -- screening factor for that pair
Examples
--------
......@@ -137,6 +140,8 @@ class AtomType(object):
# Store each NBFIX term as a dict with the atom type string matching to
# a 2-element tuple that is rmin, epsilon
self.nbfix = dict()
# Likewise, store each NBTHOLE term as a dict
self.nbthole = dict()
def __eq__(self, other):
"""
......@@ -173,6 +178,10 @@ class AtomType(object):
if epsilon14 is None: epsilon14 = epsilon
self.nbfix[typename] = (rmin, epsilon, rmin14, epsilon14)
def add_nbthole(self, typename, nbt):
""" Adds a new NBTHOLE screening factor for this atom """
self.nbthole[typename] = (nbt)
def __str__(self):
return self.name
......
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