diff --git a/arbdmodel/__init__.py b/arbdmodel/__init__.py
index 17082119bd78e8b9a9e2e82a01972cc37f1b6339..db37aac17fc76bf72bae0e2603ce3ab519811142 100644
--- a/arbdmodel/__init__.py
+++ b/arbdmodel/__init__.py
@@ -8,6 +8,7 @@ import numpy as np
from copy import copy, deepcopy
from inspect import ismethod
import os, sys, subprocess
+import shutil
_RESOURCE_DIR = Path(__file__).parent / 'resources'
def get_resource_path(relative_path):
@@ -71,7 +72,10 @@ class Parent():
self.dihedrals = []
self.impropers = []
self.exclusions = []
-
+ self.bond_angles = []
+ self.product_potentials = []
+ self.group_sites = []
+
self.rigid = False
## TODO: self.cacheInvalid = True # What will be in the cache?
@@ -148,9 +152,28 @@ class Parent():
# for b in (i,j): assert(b in beads)
self.exclusions.append( (i,j) )
+ def add_bond_angle(self, i,j,k,l, bond_angle, exclude=False):
+ assert( len(set((i,j,k,l))) == 4 )
+ ## TODO: how to handle duplicating and cloning bonds
+ # beads = [b for b in self]
+ # for b in (i,j): assert(b in beads)
+ self.bond_angles.append( (i,j,k,l, bond_angle) )
+
+ def add_product_potential(self, potential_list):
+ """ potential_list: list of tuples of form (particle_i, particle_j,..., TabulatedPotential) """
+ if len(potential_list) < 2: raise ValueError("Too few potentials")
+ for elem in potential_list:
+ beads = elem[:-1]
+ pot = elem[-1]
+ if len(beads) < 2: raise ValueError("Too few particles specified in product_potential")
+ if len(beads) > 4: raise ValueError("Too many particles specified in product_potential")
+
+ self.product_potentials.append(potential_list)
+ ## TODO: how to handle duplicating and cloning bonds
+
def get_restraints(self):
ret = []
- for c in self.children:
+ for c in self.children + self.group_sites:
ret.extend( c.get_restraints() )
return ret
@@ -200,6 +223,36 @@ class Parent():
else:
return ret
+ def get_bond_angles(self):
+ ret = self.bond_angles
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_bond_angles() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ def get_product_potentials(self):
+ ret = self.product_potentials
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_product_potentials() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ def _get_bond_potentials(self):
+ bonds = [b for i,j,b,ex in self.get_bonds()]
+ bondangles1 = [b[1] for i,j,k,l,b in self.get_bond_angles()]
+ return list(set( bonds+bondangles1 ))
+
+ def _get_angle_potentials(self):
+ angles = [b for i,j,k,b in self.get_angles()]
+ bondangles1 = [b[0] for i,j,k,l,b in self.get_bond_angles()]
+ bondangles2 = [b[2] for i,j,k,l,b in self.get_bond_angles()]
+ return list(set( angles+bondangles1+bondangles2 ))
+
+
## Removed because prohibitively slow
# def remove_duplicate_terms(self):
# for key in "bonds angles dihedrals impropers exclusions".split():
@@ -260,7 +313,7 @@ class Child():
"""
# if self.parent is not None:
- if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name is "children":
+ if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name == "children":
raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
@@ -341,7 +394,12 @@ class ParticleType():
def __init__(self, name, charge=0, parent=None, **kargs):
""" Parent type is used to fall back on for nonbonded interactions if this type is not specifically referenced """
- self.name = name
+ if parent is not None:
+ for k,v in parent.__dict__.items():
+ if k not in ParticleType.excludedAttributes:
+ self.__dict__[k] = v
+
+ self.name = name
self.charge = charge
self.parent = parent
@@ -360,6 +418,28 @@ class ParticleType():
else:
return False
+ def __getattr__(self, name):
+ """
+ Try to get attribute from the parent
+
+ """
+ if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name == "children":
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+
+ excluded_attributes = ParticleType.excludedAttributes
+ if name in excluded_attributes:
+ raise AttributeError("'{}' object has no attribute '{}' and cannot look it up from the parent".format(type(self).__name__, name))
+
+ ## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up
+ try:
+ ret = getattr(self.parent,name)
+ except:
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+ if ismethod(ret):
+ raise AttributeError("'{}' object has no method '{}'".format(type(self).__name__, name))
+ return ret
+
+
def __hash_key(self):
l = [self.name,self.charge]
for keyval in sorted(self.__dict__.items()):
@@ -584,7 +664,37 @@ class PdbModel(Transformable, Parent):
fh.write( formatString.format(**data) )
return
-
+
+ def write_pqr(self, filename):
+ if self.cacheInvalid:
+ self._updateParticleOrder()
+ with open(filename,'w') as fh:
+ ## Write header
+ fh.write("CRYST1{:>9.3f}{:>9.3f}{:>9.3f} 90.00 90.00 90.00 P 1 1\n".format( *self.dimensions ))
+
+ ## Write coordinates
+ formatString = "ATOM {idx:>6.6s} {name:^4.4s} {resname:3.3s} {chain:1.1s} {resid:>5.5s} {x:.6f} {y:.6f} {z:.6f} {charge} {radius}\n"
+ for p in self.particles:
+ data = p._get_psfpdb_dictionary()
+
+ idx = data['idx']
+ if np.log10(idx) >= 5:
+ idx = " *****"
+ else:
+ idx = "{:>6d}".format(idx)
+ data['idx'] = idx
+
+ x,y,z = p.collapsedPosition()
+ data['x'] = x
+ data['y'] = y
+ data['z'] = z
+ assert(data['resid'] < 1e5)
+ data['resid'] = "{:<4d}".format(data['resid'])
+ if 'radius' not in data:
+ data['radius'] = 2 * (data['mass']/16)**0.333333
+ fh.write( formatString.format(**data) )
+ return
+
def writePsf(self, filename):
if self.cacheUpToDate == False:
self._updateParticleOrder()
@@ -674,6 +784,29 @@ class PdbModel(Transformable, Parent):
class ArbdModel(PdbModel):
+
+ class _GroupSite():
+ """ Class to represent a collection of particles that can be used by bond potentials """
+ def __init__(self, particles, weights=None):
+ if weights is not None:
+ raise NotImplementedError
+ self.particles = particles
+ self.idx = None
+ self.restraints = []
+
+ def get_center(self):
+ c = np.array((0,0,0))
+ for p in self.particles:
+ c = c + p.collapsedPosition()
+ c = c / len(self.particles)
+ return c
+
+ def add_restraint(self, restraint):
+ self.restraints.append( restraint )
+ def get_restraints(self):
+ return [(self,r) for r in self.restraints]
+
+
def __init__(self, children, origin=None, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6,
particle_integrator = 'Brown',
cutoff=50, decomp_period=1000, pairlist_distance=None, nonbonded_resolution=0.1,
@@ -708,6 +841,13 @@ class ArbdModel(PdbModel):
self.cacheUpToDate = False
+ self.group_sites = []
+
+ def add_group_site(self, particles, weights=None):
+ g = ArbdModel._GroupSite(particles, weights)
+ self.group_sites.append(g)
+ return g
+
def clear_all(self, keep_children=False):
Parent.clear_all(self, keep_children=keep_children)
self.particles = []
@@ -715,6 +855,7 @@ class ArbdModel(PdbModel):
self.type_counts = None
self._nbParamFiles = []
self._written_bond_files = dict()
+ self.group_sites = []
def _getNbScheme(self, typeA, typeB):
scheme = None
@@ -748,8 +889,12 @@ class ArbdModel(PdbModel):
# self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
## Update particle indices
- for p,i in zip(self.particles,range(len(self.particles))):
+ for i,p in enumerate(self.particles):
p.idx = i
+
+ ## TODO recurse through childrens' group_sites
+ for i,g in enumerate(self.group_sites):
+ g.idx = len(self.particles)+i
# self.initialCoords = np.array([p.initialPosition for p in self.particles])
@@ -761,7 +906,7 @@ class ArbdModel(PdbModel):
if typeA != typeB:
self.nbSchemes.append( (nonbonded_scheme, typeB, typeA) )
- def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', restart_file=None, replicas=1, log_file=None, dry_run = False):
+ def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', restart_file=None, replicas=1, write_pqr=False, log_file=None, dry_run = False):
assert(type(gpu) is int)
num_steps = int(num_steps)
@@ -808,9 +953,10 @@ class ArbdModel(PdbModel):
self.writePdb( output_name + ".pdb" )
+ if write_pqr: self.write_pqr( output_name + ".pqr" )
self.writePsf( output_name + ".psf" )
self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period, restart_file=restart_file )
- os.sync()
+ # os.sync()
## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
@@ -828,7 +974,10 @@ class ArbdModel(PdbModel):
fd = sys.stdout if log_file is None else log_file
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
for line in process.stdout:
- fd.write(line)
+ try:
+ fd.write(line)
+ except:
+ print("WARNING: could not encode line; your locale might not be set correctly")
fd.flush()
else:
with open(log_file,'w') as fd:
@@ -855,6 +1004,9 @@ class ArbdModel(PdbModel):
self._angle_filename = "%s/%s.angles.txt" % (d, prefix)
self._dihedral_filename = "%s/%s.dihedrals.txt" % (d, prefix)
self._exclusion_filename = "%s/%s.exculsions.txt" % (d, prefix)
+ self._bond_angle_filename = "%s/%s.bondangles.txt" % (d, prefix)
+ self._product_potential_filename = "%s/%s.prodpot.txt" % (d, prefix)
+ self._group_sites_filename = "%s/%s.groups.txt" % (d, prefix)
# self._writeArbdCoordFile( prefix + ".coord.txt" )
self._writeArbdParticleFile( prefix + ".particles.txt" )
@@ -863,6 +1015,9 @@ class ArbdModel(PdbModel):
self._writeArbdAngleFile()
self._writeArbdDihedralFile()
self._writeArbdExclusionFile()
+ self._writeArbdBondAngleFile()
+ self._writeArbdProductPotentialFile()
+ self._writeArbdGroupSitesFile()
self._writeArbdPotentialFiles( prefix, directory = d )
self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod, restart_file=restart_file )
@@ -1025,15 +1180,18 @@ num {num}
{dynamics}
""".format(**particleParams))
if 'grid' in particleParams:
- if not isinstance(pt.grid, list): pt.grid = [pt.grid]
+ grids = []
+ scales = []
for g,s in pt.grid:
## TODO, use Path.relative_to?
try:
- fh.write("gridFile {}\n".format(g.relative_to(os.getcwd())))
+ grids.append(str( g.relative_to(os.getcwd()) ))
except:
- fh.write("gridFile {}\n".format(g))
+ grids.append(str(g))
+ scales.append(str(s))
- fh.write("gridFileScale {}\n".format(s))
+ fh.write("gridFile {}\n".format(" ".join(grids)))
+ fh.write("gridFileScale {}\n".format(" ".join(scales)))
else:
fh.write("gridFile {}/null.dx\n".format(self.potential_directory))
@@ -1058,13 +1216,17 @@ tabulatedPotential 1
angles = self.get_angles()
dihedrals = self.get_dihedrals()
exclusions = self.get_exclusions()
+ bond_angles = self.get_bond_angles()
+ prod_pots = self.get_product_potentials()
+ # group_sites = self.get_group_sites()
+ group_sites = self.group_sites
if len(bonds) > 0:
- for b in list(set([b for i,j,b,ex in bonds])):
+ for b in self._get_bond_potentials():
fh.write("tabulatedBondFile %s\n" % b)
if len(angles) > 0:
- for b in list(set([b for i,j,k,b in angles])):
+ for b in self._get_angle_potentials():
fh.write("tabulatedAngleFile %s\n" % b)
if len(dihedrals) > 0:
@@ -1081,6 +1243,12 @@ tabulatedPotential 1
fh.write("inputDihedrals %s\n" % self._dihedral_filename)
if len(exclusions) > 0:
fh.write("inputExcludes %s\n" % self._exclusion_filename)
+ if len(bond_angles) > 0:
+ fh.write("inputBondAngles %s\n" % self._bond_angle_filename)
+ if len(prod_pots) > 0:
+ fh.write("inputProductPotentials %s\n" % self._product_potential_filename)
+ if len(group_sites) > 0:
+ fh.write("inputGroups %s\n" % self._group_sites_filename)
write_null_dx = False
for pt,num in self.getParticleTypesAndCounts():
@@ -1147,7 +1315,7 @@ component "data" value 3
item = [i.idx]
if len(restraint) == 1:
item.append(restraint[0])
- item.extend(i.get_collapsed_position())
+ item.extend(i.collapsedPosition())
elif len(restraint) == 2:
item.append(restraint[0])
item.extend(restraint[1])
@@ -1156,7 +1324,7 @@ component "data" value 3
fh.write("RESTRAINT %d %f %f %f %f\n" % tuple(item))
def _writeArbdBondFile( self ):
- for b in list( set( [b for i,j,b,ex in self.get_bonds()] ) ):
+ for b in self._get_bond_potentials():
if type(b) is not str and not isinstance(b, Path):
b.write_file()
@@ -1169,7 +1337,7 @@ component "data" value 3
fh.write("BOND ADD %d %d %s\n" % item)
def _writeArbdAngleFile( self ):
- for b in list( set( [b for i,j,k,b in self.get_angles()] ) ):
+ for b in self._get_angle_potentials():
if type(b) is not str and not isinstance(b, Path):
b.write_file()
@@ -1194,14 +1362,57 @@ component "data" value 3
item = tuple(int(p.idx) for p in ex)
fh.write("EXCLUDE %d %d\n" % item)
+ def _writeArbdBondAngleFile( self ):
+ if len(self.bond_angles) > 0:
+ with open(self._bond_angle_filename,'w') as fh:
+ for b in self.get_bond_angles():
+ item = tuple([p.idx for p in b[:-1]] + [str(p) for p in b[-1]])
+ fh.write("BONDANGLE %d %d %d %d %s %s %s\n" % item)
+
+ def _writeArbdProductPotentialFile( self ):
+ if len(self.product_potentials) > 0:
+ with open(self._product_potential_filename,'w') as fh:
+ for pot in self.get_product_potentials():
+ line = "PRODUCTPOTENTIAL "
+ for ijk_tb in pot:
+ ijk = ijk_tb[:-1]
+ tb = ijk_tb[-1]
+ if type(tb) is tuple or type(tb) is list:
+ if len(tb) != 2: raise ValueError("Invalid product potential")
+ type_,b = tb
+ if type(type_) is not str: raise ValueError("Invalid product potential: unrecognized specification of potential type")
+ else:
+ type_ = ""
+ b = tb
+ if type(b) is not str and not isinstance(b, Path):
+ b.write_file()
+ line = line+" ".join([str(x.idx) for x in ijk])+" "
+ line = line+" ".join([str(x) for x in [type_,b] if x != ""])+" "
+ fh.write(line)
+
+ def _writeArbdGroupSitesFile( self ):
+ if len(self.group_sites) > 0:
+ with open(self._group_sites_filename,'w') as fh:
+ for i,g in enumerate(self.group_sites):
+ assert( i+len(self.particles) == g.idx )
+ ids = " ".join([str(int(p.idx)) for p in g.particles])
+ fh.write("GROUP %s\n" % ids)
+
def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
## TODO: cache coordinates using numpy arrays for quick min/max
raise(NotImplementedError)
- def write_namd_configuration( self, output_name, num_steps = 1e6,
+ def write_namd_configuration( self, output_name, minimization_steps=4800, num_steps = 1e6,
output_directory = 'output',
update_dimensions=True, extrabonds=True ):
+ num_steps = int(num_steps//12)*12
+ minimization_steps = int(minimization_steps//24)*24
+ if num_steps < 12:
+ raise ValueError("Must run with at least 12 steps")
+ if minimization_steps < 24:
+ raise ValueError("Must run with at least 24 minimization steps")
+
format_data = self.__dict__.copy() # get parameters from System object
format_data['extrabonds'] = """extraBonds on
@@ -1226,7 +1437,8 @@ tclForcesScript $prefix.forces.tcl
format_data['cell'+k] = v
format_data['prefix'] = output_name
- format_data['num_steps'] = int(num_steps//12)*12
+ format_data['minimization_steps'] = int(minimization_steps//2)
+ format_data['num_steps'] = num_steps
format_data['output_directory'] = output_directory
filename = '{}.namd'.format(output_name)
@@ -1313,9 +1525,9 @@ if {{$nLast == 0}} {{
fixedAtomsForces on
fixedAtomsFile $prefix.fixed.pdb
fixedAtomsCol B
- minimize 2400
+ minimize {minimization_steps:d}
fixedAtoms off
- minimize 2400
+ minimize {minimization_steps:d}
}} else {{
bincoordinates {output_directory}/$prefix-$nLast.restart.coor
binvelocities {output_directory}/$prefix-$nLast.restart.vel
@@ -1324,7 +1536,8 @@ if {{$nLast == 0}} {{
run {num_steps:d}
""".format(**format_data))
- def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None):
+ def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None, minimization_steps=4800, num_steps=1e6, write_pqr=False, copy_ff_from=get_resource_path("charmm36.nbfix") ):
+
if self.cacheUpToDate == False: # TODO: remove cache?
self._countParticleTypes()
self._updateParticleOrder()
@@ -1332,9 +1545,18 @@ run {num_steps:d}
if output_directory == '': output_directory='.'
self.writePdb( output_name + ".pdb" )
self.writePdb( output_name + ".fixed.pdb", beta_from_fixed=True )
+ if write_pqr: self.write_pqr( output_name + ".pqr" )
self.writePsf( output_name + ".psf" )
- self.write_namd_configuration( output_name, output_directory = output_directory )
- os.sync()
+ self.write_namd_configuration( output_name, output_directory = output_directory, minimization_steps=minimization_steps, num_steps=num_steps )
+
+ if copy_ff_from is not None and copy_ff_from != '':
+ try:
+ shutil.copytree( copy_ff_from, Path(copy_ff_from).stem )
+ except FileExistsError:
+ pass
+
+
+ # os.sync()
if not dry_run:
if namd2 is None:
diff --git a/arbdmodel/coords.py b/arbdmodel/coords.py
index 41628e83501c17098094fc12b7d4d4e6594ebcb6..6c9515fb0c410ae28cd935282212b512acd35d8d 100644
--- a/arbdmodel/coords.py
+++ b/arbdmodel/coords.py
@@ -163,17 +163,17 @@ def readArbdCoords(fname):
coords.append([float(x) for x in line.split()[1:]])
return np.array(coords)
-def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
+def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5, first_frame=0, last_frame=-1, stride=1):
import MDAnalysis as mda
usel = mda.Universe(psf, dcd)
sel = usel.select_atoms("name D*")
# r0 = ref.xyz[0,ids,:]
- ts = usel.trajectory[-1]
+ ts = usel.trajectory[last_frame]
r0 = sel.positions
pos = []
- for t in range(ts.frame-1,-1,-1):
+ for t in range(ts.frame-1,first_frame-1,-stride):
usel.trajectory[t]
R,comA,comB = minimizeRmsd(sel.positions,r0)
r = np.array( [(r-comA).dot(R)+comB for r in sel.positions] )
diff --git a/arbdmodel/interactions.py b/arbdmodel/interactions.py
index 1c4b9b6c7276d5368a01fa6a24731c9a0abb37a3..a9339882acabb531042431c72774793dc2822b6d 100644
--- a/arbdmodel/interactions.py
+++ b/arbdmodel/interactions.py
@@ -57,30 +57,28 @@ class TabulatedPotential(NonbondedScheme):
copyfile(self.tableFile, filename)
## Bonded potentials
-class HarmonicPotential():
- def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- self.k = k
+class BasePotential():
+ def __init__(self, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, zero="min", prefix="potentials/"):
self.r0 = r0
self.rRange = rRange
- self.resolution = 0.1
+ self.resolution = resolution
self.maxForce = maxForce
self.prefix = prefix
+ self.zero = zero
self.periodic = False
self.type_ = "None"
self.max_potential = max_potential
self.kscale_ = None # only used for
def filename(self):
- # raise NotImplementedError("Not implemented")
- return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
- self.k*self.kscale_, self.r0)
+ raise NotImplementedError("Not implemented")
+
+ def potential(self,dr):
+ raise NotImplementedError("Not implemented")
def __str__(self):
return self.filename()
- def potential(self, dr):
- return 0.5*self.k*dr**2
-
def write_file(self):
r = np.arange( self.rRange[0],
self.rRange[1]+self.resolution,
@@ -114,10 +112,23 @@ class HarmonicPotential():
u[0] = 0
u[1:] = np.cumsum(f*np.diff(r))
- u = u - np.min(u)
+ if self.zero == "min":
+ u = u - np.min(u)
np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )
+class HarmonicPotential(BasePotential):
+ def __init__(self, k, r0, rRange, resolution, maxForce, max_potential, zero="min", correct_geometry=False, prefix='./'):
+ self.k = k
+ self.kscale_ = None
+ BasePotential.__init__(self, r0, rRange, resolution, maxForce, max_potential, zero, prefix)
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.k*self.kscale_, self.r0)
+ def potential(self,dr):
+ return 0.5*self.k*dr**2
+
def __hash__(self):
assert(self.type_ != "None")
return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
@@ -134,21 +145,99 @@ class HarmonicPotential():
# self.kscale_ = 1.0
class HarmonicBond(HarmonicPotential):
- def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
- self.type_ = "bond"
+ def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/", zero="min", correct_geometry=False, temperature=295):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, zero=zero, correct_geometry=correct_geometry, prefix=prefix)
+ self.type_ = "gbond" if correct_geometry else "bond"
self.kscale_ = 1.0
+ self.correct_geometry = correct_geometry
+ self.temperature = temperature
+
+ def potential(self,dr):
+ u = HarmonicPotential.potential(self,dr)
+ if self.correct_geometry:
+ with np.errstate(divide='ignore',invalid='ignore'):
+ du = 2*0.58622592*np.log(dr+self.r0) * self.temperature/295
+ du[np.logical_not(np.isfinite(du))] = 0
+ u = u+du
+ return u
+
class HarmonicAngle(HarmonicPotential):
- def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, zero="min", prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, zero=zero, prefix=prefix)
self.type_ = "angle"
self.kscale_ = (180.0/np.pi)**2
class HarmonicDihedral(HarmonicPotential):
- def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, zero="min", prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, zero=zero, prefix=prefix)
self.periodic = True
self.type_ = "dihedral"
self.kscale_ = (180.0/np.pi)**2
+class WLCSKBond(BasePotential):
+ """ ## https://aip.scitation.org/doi/full/10.1063/1.4968020 """
+ def __init__(self, d, lp, kT, rRange=(0,50), resolution=0.02, maxForce=100, max_potential=None, zero="min", prefix="potentials/"):
+ BasePotential.__init__(self, 0, rRange, resolution, maxForce, max_potential, zero, prefix)
+ self.type_ = "wlcbond"
+ self.d = d # separation
+ self.lp = lp # persistence length
+ self.kT = kT
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.d, self.lp)
+ def potential(self, dr):
+ nk = self.d / (2*self.lp)
+ q2 = (dr / self.d)**2
+ a1,a2 = 1, -7.0/(2*nk)
+ a3 = 3.0/32 - 3.0/(8*nk) - 6.0/(4*nk**2)
+ p0,p1,p2,p3,p4 = 13.0/32, 3.4719,2.5064,-1.2906,0.6482
+ a4 = (p0 + p1/(2*nk) + p2*(2*nk)**-2) / (1+p3/(2*nk)+p4*(2*nk)**-2)
+ with np.errstate(divide='ignore',invalid='ignore'):
+ u = self.kT * nk * ( a1/(1-q2) - a2*np.log(1-q2) + a3*q2 - 0.5*a4*q2*(q2-2) )
+ max_force = np.diff(u[q2<1][-2:]) / np.diff(dr).mean()
+ max_u = u[q2<1][-1]
+ max_dr = dr[q2<1][-2]
+ assert( max_force >= 0 )
+ u[q2>=1] = (dr[q2>=1]-max_dr)*max_force + max_u
+ return u
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
+
+class WLCSKAngle(BasePotential):
+ ## https://aip.scitation.org/doi/full/10.1063/1.4968020
+ def __init__(self, d, lp, kT, rRange=(0,181), resolution=0.5, maxForce=None, max_potential=None, zero="min", prefix="potentials/"):
+ BasePotential.__init__(self, 180, rRange, resolution, maxForce, max_potential, zero, prefix)
+ self.type_ = "wlcangle"
+ self.d = d # separation
+ self.lp = lp # persistence length
+ self.kT = kT
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.d, self.lp)
+ def potential(self,dr):
+ nk = self.d / (2*self.lp)
+ p1,p2,p3,p4 = -1.237, 0.8105, -1.0243, 0.4595
+ C = (1 + p1*(2*nk) + p2*(2*nk)**2) / (2*nk+p3*(2*nk)**2+p4*(2*nk)**3)
+ u = self.kT * C * (1-np.cos(dr * np.pi / 180))
+ return u
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
diff --git a/arbdmodel/resources/charmm36.nbfix/par_all36_na.prm b/arbdmodel/resources/charmm36.nbfix/par_all36_na.prm
new file mode 100644
index 0000000000000000000000000000000000000000..7c63fe0de7887e51d10b7bcf05ae9cda5cf4df6f
--- /dev/null
+++ b/arbdmodel/resources/charmm36.nbfix/par_all36_na.prm
@@ -0,0 +1,1253 @@
+* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File ////
+* Alexander D. MacKerell Jr. and coworkers
+* April 2011
+* All comments to the CHARMM web site: www.charmm.org parameter
+* set discussion forum
+*
+
+!2010/2011 additions
+! ejd, 2010 RNA update
+! adm, 2011 DNA update
+! For DNA update, new atom type required for P of DNA. This required
+! replication of a number of parameters and the creation of new
+! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
+! CHARMM scripts to generate DNA will no longer work. Note that the
+! atom type change to P3 ONLY applies to the phosphodester linkage in
+! DNA and NOT to terminal phosphates, DMP etc.
+!
+!
+!references
+!
+!NUCLEIC ACIDS
+!
+!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and
+!MacKerell Jr., A.D. “Optimization of the CHARMM additive force field
+!for DNA: Improved treatment of the BI/BII conformational
+!equilibrium,†Journal of Chemical Theory and Computation, 8:348–362,
+!2012, http://dx.doi.org/10.1021/ct200723y
+!
+!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
+!“Impact of 2’-hydroxyl sampling on the conformational properties of
+!RNA: Update of the CHARMM all-atom additive force field for RNA,â€
+!JCC, In Press, 2011, NIHMSID #272247
+
+!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
+!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
+!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
+!
+!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
+!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
+!and RNA in Solution. JCC, 2000, 21: 105-120.
+!
+
+!ATOMS
+!MASS 91 HN1 1.008000 ! Nucleic acid amine proton
+!MASS 92 HN2 1.008000 ! Nucleic acid ring nitrogen proton
+!MASS 93 HN3 1.008000 ! Nucleic acid aromatic carbon proton
+!MASS 94 HN4 1.008000 ! Nucleic acid phosphate hydroxyl proton
+!MASS 95 HN5 1.008000 ! Nucleic acid ribose hydroxyl proton
+!MASS 96 HN6 1.008000 ! Nucleic acid ribose aliphatic proton
+!MASS 97 HN7 1.008000 ! Nucleic acid proton (equivalent to protein HA)
+!MASS 98 HN8 1.008000 ! Bound to CN8 in nucleic acids/model compounds
+!MASS 99 HN9 1.008000 ! Bound to CN9 in nucleic acids/model compounds
+!MASS 100 CN1 12.011000 ! Nucleic acid carbonyl carbon
+!MASS 101 CN1T 12.011000 ! Nucleic acid carbonyl carbon (T/U C2)
+!MASS 102 CN2 12.011000 ! Nucleic acid aromatic carbon to amide
+!MASS 103 CN3 12.011000 ! Nucleic acid aromatic carbon
+!MASS 104 CN3T 12.011000 ! Nucleic acid aromatic carbon, Thy C5
+!MASS 105 CN4 12.011000 ! Nucleic acid purine C8 and ADE C2
+!MASS 106 CN5 12.011000 ! Nucleic acid purine C4 and C5
+!MASS 107 CN5G 12.011000 ! Nucleic acid guanine C5
+!MASS 108 CN7 12.011000 ! Nucleic acid carbon (equivalent to protein CT1)
+!MASS 109 CN7B 12.011000 ! Nucleic acid aliphatic carbon for C1'
+!MASS 110 CN8 12.011000 ! Nucleic acid carbon (equivalent to protein CT2)
+!MASS 111 CN8B 12.011000 ! Nucleic acid carbon (equivalent to protein CT2)
+!MASS 112 CN9 12.011000 ! Nucleic acid carbon (equivalent to protein CT3)
+!MASS 113 NN1 14.007000 ! Nucleic acid amide nitrogen
+!MASS 114 NN2 14.007000 ! Nucleic acid protonated ring nitrogen
+!MASS 115 NN2B 14.007000 ! From NN2, for N9 in GUA different from ADE
+!MASS 116 NN2U 14.007000 ! Nucleic acid protonated ring nitrogen, ura N3
+!MASS 117 NN2G 14.007000 ! Nucleic acid protonated ring nitrogen, gua N1
+!MASS 118 NN3 14.007000 ! Nucleic acid unprotonated ring nitrogen
+!MASS 119 NN3A 14.007000 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
+!MASS 120 NN3G 14.007000 ! Nucleic acid unprotonated ring nitrogen, gua N3
+!MASS 121 NN4 14.007000 ! Nucleic acid purine N7
+!MASS 122 NN6 14.007000 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
+!MASS 123 ON1 15.999400 ! Nucleic acid carbonyl oxygen
+!MASS 124 ON1C 15.999400 ! Nucleic acid carbonyl oxygen, cyt O2
+!MASS 125 ON2 15.999400 ! Nucleic acid phosphate ester oxygen
+!MASS 126 ON3 15.999400 ! Nucleic acid =O in phosphate
+!MASS 127 ON4 15.999400 ! Nucleic acid phosphate hydroxyl oxygen
+!MASS 128 ON5 15.999400 ! Nucleic acid ribose hydroxyl oxygen
+!MASS 129 ON6 15.999400 ! Nucleic acid deoxyribose ring oxygen
+!MASS 130 ON6B 15.999400 ! Nucleic acid ribose ring oxygen
+!MASS 131 P 30.974000 ! phosphorus
+!MASS 132 P2 30.974000 ! phosphorus, adm, 2011 DNA update
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+!2-(aminobutyl)-1,3-propandiol terms
+CN8 NN6 200.000 1.480 ! methylammonium
+NN6 HN1 403.000 1.040 ! methylammonium
+!abasic deoxynucleoside
+ON6 CN8B 260.0 1.420 ! susil
+CN8 CN8B 222.50 1.528 ! Alkanes, sacred
+!
+CN1 CN3 302.0 1.409 !U, adm jr. 11/97
+CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
+CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
+CN1 NN2 380.0 1.367 !C, adm jr. 11/97
+CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
+CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
+CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
+CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
+CN1 NN3 350.0 1.335 !C, adm jr. 11/97
+CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
+CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
+CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
+CN2 CN3 320.0 1.406 !C, adm jr. 11/97
+CN2 CN5 360.0 1.358 !A, adm jr. 11/97
+CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
+CN2 NN2G 400.0 1.392 !G
+CN2 NN3 450.0 1.343 !C
+CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
+CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
+CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
+CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
+CN3T CN9 230.0 1.478 !T, adm jr. 11/97
+CN3 HN3 350.0 1.09 !C,U, JWK
+CN3T HN3 350.0 1.09 !T, JWK
+CN3 NN2 302.0 1.343 !C, adm jr. 11/97
+CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
+CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
+CN4 NN2 320.0 1.374 !A, adm jr. 11/97
+CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
+CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
+CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
+CN5 CN5 310.0 1.361 !A, adm jr. 11/97
+CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
+CN5 NN2 300.0 1.375 !A, adm jr. 11/97
+CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
+CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
+CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
+CN5 NN4 310.0 1.355 !A, adm jr. 11/97
+CN5G NN4 310.0 1.365 !G, adm jr. 11/97
+CN8 CN8 222.50 1.528 !Alkanes, sacred
+CN8 CN9 222.50 1.528 !Alkanes, sacred
+CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
+CN8 ON5 428.0 1.42 !RIBOSE, MeOH
+CN9 HN9 322.0 1.111 !alkanes
+CN9 ON2 340.0 1.43 !DMP, ADM Jr.
+HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
+HN2 NN2 474.0 1.01 !C,U, JWK
+HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
+HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
+HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
+HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
+ON2 P 270.0 1.60 !DMP, ADM Jr.
+ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update
+ON3 P 580.0 1.48 !DMP, ADM Jr.
+ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update
+ON4 P 237.0 1.58 !MP_1, ADM Jr.
+ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update
+!NN5 HN1 460.0 1.01 !sugar model, adm jr.
+!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
+CN7B ON6 260.0 1.420 ! From exp
+CN7B CN8 200.0 1.518 ! From exp
+CN7 ON6 240.0 1.446 ! Fom exp.
+CN7 CN7 222.5 1.529 ! From exp
+CN7 CN8 222.5 1.516 ! From exp.
+CN7 CN9 222.5 1.516 ! for 5MET, From alkanes
+CN7 HN7 309.0 1.111 !Alkanes, sacred
+CN8 HN8 309.0 1.111 !Alkanes, sacred
+CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
+!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
+!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
+CN7B ON6B 260.0 1.420 ! From CN7B ON6
+CN7 ON6B 240.0 1.480 ! From CN7 ON6
+CN7B CN7B 200.0 1.450 !
+CN7 CN7B 222.5 1.460 ! Specific to RNA
+!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
+CN7 CN8B 222.5 1.512 ! From exp.
+CN8B ON2 320.0 1.44 ! From exp
+!CN8B ON5 250.0 1.44 ! From CN8B ON2
+CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
+CN7 ON2 310.0 1.433 ! From exp
+CN7B ON2 310.0 1.433 ! From exp, for NADPH and bkbmod
+!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
+CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
+! C1'-N9 (purines)/C1'-N1 (pyrimidines)
+CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
+CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
+CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
+CN7B NN2 220.0 1.456 !A/C
+CN7B NN2B 220.0 1.458 !G/T/U
+! C5'-H in model compounds and DNA
+CN8B HN8 309.0 1.111 !Alkanes, sacred
+ON5 HN5 545.0 0.960 !RIBOSE, MeOH
+!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
+!CN7B ON5 250.0 1.400 ! From CN7 ON5
+CN7B ON5 428.0 1.400 ! check adm jr.,
+!FC should be 428.000 based on Meoh
+!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
+
+!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
+CN8 ON2 340.0 1.44 !
+!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types Ktheta Theta0 Kub S0
+!
+! angle parameters have been rearranged based on model
+! compounds and functional groups. Additional angle
+! parameters follow sorted based on the central atom
+!
+!2-(aminobutyl)-1,3-propandiol terms
+CN7 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
+CN8 CN7 CN8 58.35 113.60 11.16 2.561 !alkane
+CN8 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
+HN1 NN6 CN8 30.00 109.50 20.00 2.074 !methylammonium
+NN6 CN8 HN8 45.00 107.50 35.00 2.101 !methylammonium
+CN7 CN8 ON2 115.00 109.70 !DNA exocyclic angles
+NN6 CN8 CN8 67.70 110.00 !methylammonium
+HN1 NN6 HN1 44.00 109.50 !methylammonium
+!abasic propyl linkage
+ON2 CN8 CN8 115.0 109.7 !DNA exocyclic angles
+!abasic deoxynucleoside
+CN7 ON6 CN8B 110.0 109.0
+ON6 CN8B CN8 90.0 106.0
+CN8B CN8 CN7 80.0 106.0
+ON6 CN8B HN8 45.2 107.24 !
+HN8 CN8B CN8 34.53 110.10 22.53 2.179 ! alkane
+HN8 CN8 CN8B 34.53 110.10 22.53 2.179 ! alkane
+
+! pyrmidines
+!@@@@@@@@ Adenine
+! ade 6-mem ring
+CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97
+NN3A CN4 NN3A 60.0 133.0 !6R)
+CN4 NN3A CN5 90.0 110.1 !6R)
+CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4
+CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5
+CN5 CN2 NN3A 60.0 110.7 !6R)
+CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4
+CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5
+CN4 NN4 CN5 120.0 104.6 !5R)
+NN2 CN4 NN4 100.0 113.4 !5R)
+CN4 NN2 CN5 100.0 106.3 !5R)
+NN2 CN5 NN3A 100.0 126.9 !bridgeC4
+CN2 CN5 NN4 100.0 129.0 !bridgeC5
+HN3 CN4 NN3A 38.0 113.5 !h2
+NN3A CN2 NN1 50.0 130.7 !n6
+CN5 CN2 NN1 50.0 118.6 !
+CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G
+HN1 NN1 HN1 31.0 117.0 !C,A,G
+NN4 CN4 HN3 39.0 124.8 !h8, G,A
+NN2 CN4 HN3 39.0 121.8 !
+CN5 NN2 HN2 30.0 129.4 !h9
+CN4 NN2 HN2 30.0 125.0 !
+!@@@@@@@@ Guanine
+! gua 6-mem ring
+CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97
+NN2G CN2 NN3G 70.0 122.2 !6R)
+CN2 NN3G CN5 90.0 109.4 !6R)
+CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4
+CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5
+CN5G CN1 NN2G 70.0 107.8 !6R)
+CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4
+CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5
+CN4 NN4 CN5G 120.0 103.8 !5R)
+NN2B CN4 NN4 100.0 113.0 !5R)
+CN4 NN2B CN5 100.0 107.2 !5R)
+NN2B CN5 NN3G 140.0 125.5 ! bridgeC4
+CN1 CN5G NN4 125.0 129.0 ! bridgeC5
+CN1 NN2G HN2 45.0 113.3 ! h1
+CN2 NN2G HN2 45.0 115.6 !
+NN1 CN2 NN2G 95.0 115.4 ! n2
+NN1 CN2 NN3G 95.0 122.4 !
+NN2G CN1 ON1 50.0 127.5 ! o6
+CN5G CN1 ON1 50.0 124.7 !
+HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8)
+CN4 NN2B HN2 30.0 124.6 ! h9
+CN5 NN2B HN2 30.0 129.3 !
+!@@@@@@@@ Cytosine
+! cyt 6-mem ring
+CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97
+NN2 CN1 NN3 50.0 116.8 !C
+CN1 NN3 CN2 85.0 119.1 !C
+CN3 CN2 NN3 85.0 119.3 !C
+CN2 CN3 CN3 85.0 117.8 !C
+CN3 CN3 NN2 85.0 122.9 !C
+CN1 NN2 HN2 37.0 121.2 !C, h1
+CN3 NN2 HN2 37.0 114.7 !C
+NN2 CN1 ON1C 130.0 119.4 !C, o2
+NN3 CN1 ON1C 130.0 123.8 !C
+NN3 CN2 NN1 81.0 122.3 !C, n4
+CN3 CN2 NN1 81.0 118.4 !C
+CN2 CN3 HN3 38.0 120.1 !C h5
+CN3 CN3 HN3 38.0 122.1 !C,U
+HN3 CN3 NN2 44.0 115.0 !C, h6
+!@@@@@@@@ Uracil
+! ura 6-mem ring
+CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97
+NN2B CN1T NN2U 50.0 114.0 !U
+CN1T NN2U CN1 50.0 130.2 !U
+NN2U CN1 CN3 70.0 112.6 !U
+CN1 CN3 CN3 100.0 117.6 !U
+CN3 CN3 NN2B 100.0 123.6 !U
+CN1T NN2B HN2 40.5 122.0 !U, h1
+CN3 NN2B HN2 32.0 116.0 !U
+NN2B CN1T ON1 100.0 121.6 !U, o2
+NN2U CN1T ON1 100.0 124.4 !U
+CN1T NN2U HN2 40.5 114.4 !U, h3
+CN1 NN2U HN2 40.5 115.4 !U
+NN2U CN1 ON1 100.0 121.9 !U, o4
+CN3 CN1 ON1 100.0 125.5 !U,
+CN1 CN3 HN3 30.0 120.3 !U, h5
+HN3 CN3 NN2B 30.0 114.3 !U, h6
+! thymine 6-mem ring (unique from ura)
+CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97
+CN1 CN3T CN3 120.0 116.7 !T
+CN3T CN3 NN2B 120.0 123.6 !125.3 !T
+CN3T CN1 ON1 100.0 124.6 !T, o4
+CN1 CN3T CN9 38.0 118.7 !T, c5 methyl
+CN3 CN3T CN9 38.0 124.6 !T
+CN3T CN3 HN3 30.0 122.1 !T, h6
+! base to methyl connection
+CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr.
+CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91
+CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr.
+CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91
+CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr.
+CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr.
+CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr.
+CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr.
+CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr.
+CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr.
+NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr.
+!===== For glycosydic linkage, base to c1'
+CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A
+CN3 NN2B CN7B 45.0 119.6 !U/T
+CN1 NN2 CN7B 45.0 120.0 !C, FC from A
+CN3 NN2 CN7B 45.0 115.9 !C
+CN5 NN2 CN7B 45.0 126.1 !A
+CN4 NN2 CN7B 45.0 127.6 !A
+CN5 NN2B CN7B 45.0 126.5 !G
+CN4 NN2B CN7B 45.0 126.3 !G
+ON6 CN7B NN2 110.0 108.0 !C/A DNA
+ON6B CN7B NN2 110.0 112.0 !C/A RNA
+CN8 CN7B NN2 110.0 113.7 !C/A
+CN7B CN7B NN2 110.0 111.0 !C/A, RNA
+ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A
+ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A
+CN8 CN7B NN2B 110.0 113.7 !T/U/G
+CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA
+HN7 CN7B NN2 43.0 111.0 !
+HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2
+!===== End of glycosydic linkage
+! remaining terms ordered based on central atom
+CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred
+CN9 CN7 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred
+HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM
+HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH
+CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
+CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
+CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred
+HN9 CN9 CN7 33.43 110.1 22.53 2.179 ! Alkanes, sacred
+HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr.
+HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr.
+HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr.
+HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr.
+!HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr.
+CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr.
+HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr.
+HN4 ON4 P2 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. , adm, 2011 DNA update
+HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH
+HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH
+ON2 P ON2 80.0 104.3 !DMP, ADM Jr.
+ON2 P2 ON2 80.0 104.3 !DMP, ADM Jr., adm, 2011 DNA update
+ON2 P ON4 48.1 108.0 !MP_1, ADM Jr.
+ON2 P2 ON4 48.1 108.0 !MP_1, ADM Jr., adm, 2011 DNA update
+ON3 P ON4 98.9 108.23 !MP_1, ADM Jr.
+ON3 P2 ON4 98.9 108.23 !MP_1, ADM Jr., adm, 2011 DNA update
+ON4 P ON4 98.9 104.0 !MP_0, ADM Jr.
+ON4 P2 ON4 98.9 104.0 !MP_0, ADM Jr., adm, 2011 DNA update
+CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH
+HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92
+!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
+CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1'
+ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1'
+CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3'
+CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4'
+CN9 CN7 CN7 60.00 102.0 8.0 2.561 !for 5MET, adm jr.
+CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4'
+HN7 CN7 ON6 45.2 107.24 !
+HN7 CN7B ON6 45.2 107.24 !
+HN7 CN7 CN7 40.0 108.00 !
+CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly
+CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes
+HN7 CN7 CN8 34.5 110.1 22.53 2.179 !
+HN8 CN8 CN7 34.53 110.10 22.53 2.179 !
+HN8 CN8 CN8 34.53 110.10 22.53 2.179 !
+HN8 CN8 HN8 35.5 109.00 5.40 1.802 !
+HN7 CN7 HN7 35.5 109.00 5.40 1.802 !
+!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@
+
+!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
+CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B
+CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6
+ON6B CN7B CN7B 90.0 106.0 ! 030998
+CN7B CN7B CN7 110.0 96.0 !
+CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4'
+HN7 CN7 ON6B 45.2 107.24 !
+HN7 CN7B ON6B 45.2 107.24 !
+CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly
+HN7 CN7B HN7 35.5 109.00 5.40 1.802 !
+!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@
+
+!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
+ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5'
+ON6 CN7 CN9 90.0 108.2 !for 5MET, adm jr.
+CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5'
+CN8 CN7 CN8B 58.35 113.60 11.16 2.561 ! from alkane, 25P1
+CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5'
+CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3'
+CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH and bkbmod
+CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3'
+CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P
+CN8B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P, adm, 2011 DNA update
+CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P
+CN7 ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, adm, 2011 DNA update
+CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod
+CN7B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod, adm, 2011 DNA update
+! sugar
+HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8
+HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2
+HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8
+HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred
+HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred
+HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2
+HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH and bkbmod
+!===== For 5ter patch:
+CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5
+CN8B CN7 ON5 90.0 108.2 ! phosphoramidate, carbocyclic
+HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5
+!===== For 3ter patch:
+ON5 CN7 CN8 75.7 110.0 ! from CHARMM22
+ON5 CN7 CN7 75.7 110.1 !
+HN7 CN7 ON5 60.0 109.5 !
+HN5 ON5 CN7 57.5 109.0 !
+!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@
+
+!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
+!O4'-C4'-C5'
+ON6B CN7 CN8B 90.0 108.2 !
+ON6B CN7 CN9 90.0 108.2 ! for 5MET patch, adm jr.
+!O3'-C3'-C2'
+ON2 CN7 CN7B 90.0 110.0 !
+ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8
+!O2'-C2'-C1'
+ON5 CN7B CN7B 80.0 108.4 !
+!O2'-C2'-C3'
+ON5 CN7B CN7 90.0 108.0 !
+HN7 CN7B ON5 60.0 109.5 !
+HN5 ON5 CN7B 57.5 109.0 !
+HN7 CN7B CN7 34.53 110.10 22.53 2.179
+HN7 CN7 CN7B 34.53 110.10 22.53 2.179
+
+!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@
+
+!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
+CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr.
+CN8 ON2 P2 20.0 120.0 35. 2.33 !DMP, adm jr., adm 2011 DNA update
+!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
+ON2 P ON3 98.9 111.6 !DMP, adm jr.
+ON2 P2 ON3 98.9 111.6 !DMP, adm jr., adm, 2011 DNA update
+ON3 P ON3 120.0 120.0 !DMP, adm jr.
+ON3 P2 ON3 120.0 120.0 !DMP, adm jr., adm, 2011 DNA update
+HN8 CN8 ON2 60.0 109.5 !DMP, adm jr.
+ON5 P ON3 98.9 111.6 ! From ON2 P ON3
+!------------------------ added for araim ----------------------
+ON6 CN7B CN7 120.0 106.25 !
+CN7B CN7 CN8 58.35 113.6 11.16 2.561 !
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!2-(aminobutyl)-1,3-propandiol terms
+X CN8 ON2 X -0.10 3 0.0 ! phosphate ester
+X CN7 CN8 X 0.20 3 0.0 ! alkane
+X CN8 NN6 X 0.10 3 0.0 ! methylammonium
+!abasic nucleoside terms - susil
+CN7 ON6 CN8B HN8 0.195 1 0.0
+ON6 CN8B CN8 HN8 0.195 1 0.0
+HN7 CN7 ON6 CN8B 0.195 3 0.0
+CN8B CN8 CN7 HN7 0.195 3 0.0
+HN8 CN8B CN8 HN8 0.195 3 0.0
+HN8 CN8B CN8 CN7 0.195 3 0.0
+! c5'-c4'-o4'-c1', exo
+CN8B CN7 ON6 CN8B 0.5 5 0.0 ! min at 150 310 max at 25 200
+CN8B CN7 ON6 CN8B 0.1 3 180.0
+CN8B CN7 ON6 CN8B 0.5 1 0.0
+! c1'-c2'-c3'-o3', exo
+CN8B CN8 CN7 ON5 0.4 5 0.0
+CN8B CN8 CN7 ON5 0.4 3 0.0
+CN8B CN8 CN7 ON5 0.7 2 0.0 !elevates energy at 0 (c3'endo), adm
+CN8B CN8 CN7 ON5 0.5 1 180.0 !elevates energy at 0 (c3'endo), adm
+CN8B CN8 CN7 ON2 0.4 5 0.0 !terms for oligonuclotide
+CN8B CN8 CN7 ON2 0.4 3 0.0
+CN8B CN8 CN7 ON2 0.7 2 0.0
+CN8B CN8 CN7 ON2 0.5 1 180.0
+! c4'-o4'-c1'-c2', tau0
+CN7 ON6 CN8B CN8 0.6 6 180.0
+CN7 ON6 CN8B CN8 0.6 3 0.0
+! o4'-c1'-c2'-c3', tau1
+ON6 CN8B CN8 CN7 0.7 5 180.0 !lowers 90, shifts c2endo minimum towards 200
+ON6 CN8B CN8 CN7 0.4 4 0.0 !lowers 90, shifts c2endo minimum towards 200
+ON6 CN8B CN8 CN7 0.4 3 180.0 !lowers 90, shifts c2endo minimum towards 200
+! c4'-c3'-c2'-c1', tau2
+CN7 CN7 CN8 CN8B 0.5 4 0.0
+CN7 CN7 CN8 CN8B 0.1 3 0.0 !lowers energy in 150 to 250 range
+! c1'-o4'-c4'-c3', tau4
+CN8B ON6 CN7 CN7 0.5 3 0.0 !effects surface in 200-360 region
+
+! PHOSPHATE
+ON2 P2 ON2 CN7 0.90 1 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2 P2 ON2 CN7 0.40 2 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2 P2 ON2 CN7 0.20 3 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
+ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr.
+ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr.
+ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr.
+ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr.
+ON2 P2 ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
+ON2 P2 ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
+ON2 P2 ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
+ON2 P2 ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr., adm 2011 DNA update
+! Added when C5' defined as CN8B (NF 041497):
+ON2 P2 ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2 P2 ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2 P2 ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2 P2 ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., adm, 2011 DNA update
+ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., RNA
+ON2 P ON2 CN9 1.20 1 180.0 !dmp
+ON2 P ON2 CN9 0.10 2 180.0 !dmp
+ON2 P ON2 CN9 0.10 3 180.0 !dmp
+ON2 P ON2 CN9 0.00 6 0.0 !dmp
+ON2 P2 ON2 CN9 1.20 1 180.0 !dmp, adm, 2011 DNA update
+ON2 P2 ON2 CN9 0.10 2 180.0 !dmp, adm, 2011 DNA update
+ON2 P2 ON2 CN9 0.10 3 180.0 !dmp, adm, 2011 DNA update
+ON2 P2 ON2 CN9 0.00 6 0.0 !dmp, adm, 2011 DNA update
+!
+ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3'
+ON3 P2 ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3', adm, 2011 DNA update
+ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH and bkbmod
+ON3 P ON2 CN8 0.10 3 0.0 !dmp
+ON3 P2 ON2 CN8 0.10 3 0.0 !dmp, adm 2011 DNA update
+ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5'
+ON3 P2 ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5', adm, 2011 DNA update
+ON3 P ON2 CN9 0.10 3 0.0 !dmp
+ON3 P2 ON2 CN9 0.10 3 0.0 !dmp, adm, 2011 DNA update
+! terminal phosphate terms, adm jr.
+ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr.
+ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr.
+ON4 P2 ON2 CN7 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
+ON4 P2 ON2 CN7 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
+ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr.
+ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr.
+ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr.
+ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr.
+ON4 P2 ON2 CN8B 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
+ON4 P2 ON2 CN8B 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
+ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr.
+ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr.
+ON4 P2 ON2 CN9 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
+ON4 P2 ON2 CN9 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
+X ON4 P X 0.30 3 0.0 !MP_1, adm jr.
+X ON4 P2 X 0.30 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
+! When O5' is ON2 (phosphodiester linkage):
+P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P
+P2 ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P, adm, 2011 DNA update
+P ON2 CN7B HN7 0.000 3 0.0 !for NADPH and bkbmod
+P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P
+P2 ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P, adm, 2011 DNA update
+P ON2 CN8 HN8 0.000 3 0.0 !dmp
+P ON2 CN9 HN9 0.000 3 0.0 !dmp
+P2 ON2 CN9 HN9 0.000 3 0.0 !dmp, adm, 2011 DNA update
+! butane gauche terms
+cn9 cn8 cn8 cn9 0.15 1 0.0
+cn9 cn8 cn8 cn8 0.15 1 0.0
+! BASES
+! Uracil
+NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97
+CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97
+NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97
+CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97
+CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97
+CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97
+HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97
+HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97
+ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97
+ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
+ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
+HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97
+NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
+CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
+CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
+NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
+!Thymine
+CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97
+NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97
+CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97
+NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
+NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
+CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
+CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
+CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97
+! Cytosine
+CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97
+NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97
+CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97
+NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97
+CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97
+CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97
+NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
+CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
+NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97
+NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97
+NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97
+ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97
+ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97
+ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97
+NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
+NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
+CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
+CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
+X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97
+! Adenine
+CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem
+NN3A CN4 NN3A CN5 2.0 2 180.0 !
+CN4 NN3A CN5 CN5 1.8 2 180.0 !
+NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x
+CN5 CN5 CN2 NN3A 1.8 2 180.0 !
+CN5 CN2 NN3A CN4 10.0 2 180.0 !
+CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem
+CN5 NN4 CN4 NN2 14.0 2 180.0 !
+NN4 CN4 NN2 CN5 6.0 2 180.0 !
+CN4 NN2 CN5 CN5 6.0 2 180.0 !
+NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x
+CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2
+CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2
+CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8
+CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8
+CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9
+NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9
+HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9
+CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6
+CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6
+NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6
+CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2
+NN3A CN2 NN1 HN1 0.5 2 180.0 !
+! Butterfly motion
+NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97
+CN2 CN5 CN5 NN2 7.0 2 180.0 !A
+NN3A CN2 CN5 NN4 2.0 2 180.0 !A
+CN2 CN5 NN4 CN4 2.0 2 180.0 !A
+CN4 NN3A CN5 NN2 2.0 2 180.0 !A
+NN3A CN5 NN2 CN4 2.0 2 180.0 !A
+! Guanine
+CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem
+NN2G CN2 NN3G CN5 2.0 2 180.0 !
+CN2 NN3G CN5 CN5G 0.2 2 180.0 !
+NN3G CN5 CN5G CN1 2.0 2 180.0 !
+CN5 CN5G CN1 NN2G 0.2 2 180.0 !
+CN5G CN1 NN2G CN2 0.2 2 180.0 !
+CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem
+CN5G NN4 CN4 NN2B 16.0 2 180.0 !
+NN4 CN4 NN2B CN5 6.0 2 180.0 !
+CN4 NN2B CN5 CN5G 6.0 2 180.0 !
+NN2B CN5 CN5G NN4 10.0 2 180.0 !
+! substitutents
+ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6
+ON1 CN1 CN5G NN4 0.0 2 180.0 !
+ON1 CN1 NN2G CN2 14.0 2 180.0 !
+ON1 CN1 NN2G HN2 0.0 2 180.0 !
+NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2
+NN1 CN2 NN3G CN5 4.0 2 180.0 !
+NN1 CN2 NN2G HN2 0.0 2 180.0 !
+NN2G CN2 NN1 HN1 1.2 2 180.0 !
+NN3G CN2 NN1 HN1 1.2 2 180.0 !
+HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1
+HN2 NN2G CN2 NN3G 3.6 2 180.0 !
+HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8
+HN3 CN4 NN2B CN5 5.6 2 180.0 !
+HN3 CN4 NN2B HN2 0.0 2 180.0 !
+HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9
+HN2 NN2B CN5 NN3G 1.2 2 180.0 !
+HN2 NN2B CN4 NN4 1.2 2 180.0 !
+! Butterfly motion
+NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97
+CN1 CN5G CN5 NN2 10.0 2 180.0 !
+NN2G CN1 CN5G NN4 2.0 2 180.0 !
+CN1 CN5G NN4 CN4 2.0 2 180.0 !
+CN2 NN3G CN5 NN2B 2.0 2 180.0 !
+NN3G CN5 NN2B CN4 2.0 2 180.0 !
+! Wild cards for uracil, thymine and cytosine
+X CN1 NN3 X 1.0 2 180.0 ! c22
+X CN1 NN2 X 0.9 2 180.0 ! c22
+X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines
+X CN1 NN2G X 0.9 2 180.0 ! c22
+X CN1 NN2U X 0.9 2 180.0 ! c22
+X CN1T NN2U X 0.9 2 180.0 ! c22
+X CN3 NN2 X 1.0 2 180.0 ! c22
+X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines
+X CN3 CN3 X 1.0 2 180.0 ! c22
+X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
+X CN1 CN3 X 1.0 2 180.0 ! c22
+X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
+X CN2 CN3 X 0.8 2 180.0 ! c22
+! Wild cards for adenine and guanine
+X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97
+X CN2 NN2G X 1.0 2 180.0 !
+X CN2 CN5 X 1.0 2 180.0 !
+X CN4 NN2 X 1.5 2 180.0 !
+X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X
+X CN4 NN3A X 3.5 2 180.0 !
+X CN4 NN4 X 2.0 2 180.0 ! A,G
+X CN5 CN5 X 0.0 2 180.0 !
+X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97
+X CN5 NN2 X 1.5 2 180.0 !
+X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X
+X CN5 NN3A X 1.0 2 180.0 !
+X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97
+X CN5 NN4 X 1.0 2 180.0 !
+X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97
+X CN2 NN3A X 1.0 2 180.0 !
+X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97
+! MISC.
+CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C
+CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C
+CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A
+CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A
+CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U
+CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T
+CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U
+CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G
+CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G
+CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G
+CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G
+CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G
+CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G
+X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
+X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
+!for nadp/nadph, adm jr.
+HN7 CN7B CN7B ON2 0.195 3 0.0 !for NADPH and bkbmod
+ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH and bkbmod
+
+! sugar, replace with ribose terms 021998
+CN7 CN7B ON6 CN7 0.6 6 180.0
+CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes
+CN7B CN7 CN7 CN9 0.4 6 0.0 ! good for amplitudes, 5MET
+CN7 CN7 CN7 ON6 0.6 6 0.0
+CN7 CN7 CN7B ON6 0.6 6 0.0
+ON2 CN7 CN7 CN7 0.8 6 0.0 !
+ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
+ON2 CN7 CN7 CN7 2.0 3 180.0 !
+! for ndph
+ON2 CN7B CN7 CN7 0.8 6 0.0 !
+ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right
+ON2 CN7B CN7 CN7 2.0 3 180.0 !
+!
+ON5 CN7 CN7 CN7 0.8 6 0.0 !
+ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
+ON5 CN7 CN7 CN7 2.0 3 180.0 !
+ON5 CN7 CN7 ON5 0.0 3 0.0 !
+ON5 CN7 CN7 ON2 0.0 3 0.0 !
+ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes
+ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes
+ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo
+ON2 CN7 CN7B ON6 0.2 3 0.0 !
+CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
+
+!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
+! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
+! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
+!@@@@@@ Begining of chi
+!============= added for torsion about chi in adenine ============
+!For link from sugar to base:
+CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF
+CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr.
+CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr.
+CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr.
+!For chi itself:
+ !DNA:
+ON6 CN7B NN2 CN5 1.1 1 180.0 !
+ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF
+ !RNA:
+ON6B CN7B NN2 CN5 1.1 1 180.0 !
+ON6B CN7B NN2 CN4 1.1 1 0.0 !
+ !DNA:
+CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF
+CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF
+ !RNA:
+CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF
+CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF
+
+HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF
+HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF
+!@@@@@@ End of chi in adenines
+
+!============== terms for torsion about chi in cytosines ===========
+CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF
+CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A
+CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr.
+CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr.
+ !DNA:
+ON6 CN7B NN2 CN1 0.0 3 0.0 !
+ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF
+ !RNA:
+ON6B CN7B NN2 CN1 0.0 3 0.0 !
+ON6B CN7B NN2 CN3 1.0 1 0.0 !
+ !DNA:
+CN8 CN7B NN2 CN1 1.0 3 0.0 !
+CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697
+ !RNA:
+CN7B CN7B NN2 CN1 1.0 3 0.0 !
+CN7B CN7B NN2 CN3 0.0 3 180.0 !
+
+HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF
+HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF
+!@@@@@@ End of chi in cytosines
+
+!=========== terms for torsion about chi in uracils/thymines ===========
+CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF
+CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A
+CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr.
+CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr.
+ !DNA:
+ON6 CN7B NN2B CN1 0.0 3 0.0 !
+ON6 CN7B NN2B CN1T 0.7 3 0.0 !
+ON6 CN7B NN2B CN1T 0.8 1 180.0 !
+ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF
+ !RNA:
+ON6B CN7B NN2B CN1 0.0 3 0.0 !
+ON6B CN7B NN2B CN1T 0.7 3 0.0 !
+ON6B CN7B NN2B CN1T 0.8 1 180.0 !
+ON6B CN7B NN2B CN3 0.9 1 0.0 !
+ !DNA:
+CN8 CN7B NN2B CN1T 0.2 3 180.0 !
+CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF
+ !RNA:
+CN7B CN7B NN2B CN1T 0.2 3 180.0 !
+CN7B CN7B NN2B CN3 0.0 3 180.0 !
+
+HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF
+HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF
+!@@@@@@ End of chi in thymines
+
+!============= added for torsion about chi in guanine ============
+CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF
+CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr.
+CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U
+CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr.
+ !DNA:
+ON6 CN7B NN2B CN5 0.2 3 0.0 !
+ON6 CN7B NN2B CN5 1.1 1 180.0 !
+ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF
+ !RNA:
+ON6B CN7B NN2B CN5 0.2 3 0.0 !
+ON6B CN7B NN2B CN5 1.1 1 180.0 !
+ON6B CN7B NN2B CN4 1.4 1 0.0 !
+ !DNA:
+CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF
+CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697
+ !RNA:
+CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF
+CN7B CN7B NN2B CN4 0.0 3 180.0 !
+
+HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF
+HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF
+!@@@@@@ End of chi in guanines
+!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
+ !DNA:
+CN7 ON6 CN7B NN2 0.0 3 0.0
+CN7 ON6 CN7B NN2B 0.0 3 0.0
+ !RNA:
+CN7 ON6B CN7B NN2 0.0 3 0.0
+CN7 ON6B CN7B NN2B 0.0 3 0.0
+ !DNA:
+CN7 CN8 CN7B NN2 0.0 3 0.0
+CN7 CN8 CN7B NN2B 0.0 3 0.0
+HN8 CN8 CN7B NN2 0.0 3 0.0
+HN8 CN8 CN7B NN2B 0.0 3 0.0
+ !RNA:
+CN7 CN7B CN7B NN2 0.0 3 0.0
+CN7 CN7B CN7B NN2B 0.0 3 0.0
+ !RNA
+HN7 CN7B CN7B NN2 0.0 3 0.0
+HN7 CN7B CN7B NN2B 0.0 3 0.0
+
+!@@@@@@ Begining of torsions involving exocyclic sugar atoms:
+!======= CN7 CN8B ON2 P = C4'-C5'-O5'-P
+CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr.
+CN7 CN8B ON2 P2 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr., adm, 2011 DNA update
+! the following differ significantly from the alcohols
+! in the protein (based on ethanol), they also differ from other
+! NA C-C-OH-H parameters (see below)
+! The two following terms have been replaced by their ethanol
+! counterpart (NF, 083098)
+CN7 CN8B ON5 HN5 1.3300 1 0.00
+CN7 CN8B ON5 HN5 0.1800 2 0.00
+CN7 CN8B ON5 HN5 0.3200 3 0.00
+!======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta
+HN8 CN8B ON5 HN5 0.0 3 0.0 !bet
+!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
+! When O5' is ON2 (phosphodiester linkage):
+CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr.
+CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
+CN7 CN7 CN8B ON2 0.40 2 0.0 !gam
+CN7 CN7 CN8B ON2 2.50 1 180.0 !gam
+!
+CN8 CN7 CN8B ON2 0.2 3 180.0 ! from gam, carbocyclic and 25P1
+! When O5' is ON5 (5TER patch):
+CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr.
+CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
+CN7 CN7 CN8B ON5 0.40 2 0.0 !gam
+CN7 CN7 CN8B ON5 2.50 1 180.0 !gam
+!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
+! When O5' is ON2 (3'-5' phosphodiester linkage)
+ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60
+ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA
+! When O5' is ON5 (5TER patch):
+ON6 CN7 CN8B ON5 3.4 1 180.0 !gam
+ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA
+!======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H
+HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H
+HN8 CN8B CN7 CN8 0.195 1 0.0 !gam, carbocylic, 25P1
+!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
+HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
+HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA
+!======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5'
+! When O5' is ON2 (phosphodiester linkage):
+HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5'
+! When O5' is ON5 (5TER patch):
+HN7 CN7 CN8B ON5 0.195 3 0.0 !gam
+HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
+! terms for 5MET patch
+CN9 CN7 CN7 CN8B 0.5 4 180.0 !cn8 -> cn9
+HN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
+CN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
+ON6 CN7 CN9 HN9 0.195 3 0.0 !cn7 -> cn9
+HN7 CN7 CN7 CN9 0.195 3 0.0 !cn8 -> cn9
+ON2 CN7 CN7 CN9 0.2 4 0.0 !cn8b -> cn9
+ON2 CN7 CN7 CN9 0.8 3 180.0 !cn8b -> cn9
+CN8 CN7 CN7 CN9 0.5 4 180.0 !cn8b -> cn9
+
+!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
+! This term is well suited to modify the puckering surfaces, in
+! particular because it is present in THF5P
+CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
+CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA
+!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3'
+! These terms affect the c2endo/c3endo energy difference
+! When O3' is ON2 (3'-5' phosphodiester linkage)
+ON2 CN7 CN7 CN8B 0.2 4 0.0 !del
+! the following term controls the location of the barrier at ~75 deg.
+ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250]
+! When O3' is ON5 (patch 3TER)
+ON5 CN7 CN7 CN8B 0.2 4 0.0 !
+ON5 CN7 CN7 CN8B 0.8 3 180.0 !
+!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3'
+! These terms contribute to delta
+! These terms are present in THF3P and THFM3P but not in THF5P
+! When O3' is ON2 (3'-5' phosphodiester linkage)
+ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes
+ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes
+ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo
+ON2 CN7 CN7 ON6 0.2 3 0.0 !
+ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
+ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
+ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
+ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
+! for ndph: make identical to ON2 CN7 CN7 ON6B
+ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
+ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
+ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
+ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
+! When O3' is ON5 (patch 3TER)
+ON5 CN7 CN7 ON6 0.5 6 0.0 !
+ON5 CN7 CN7 ON6 0.3 5 0.0 !
+ON5 CN7 CN7 ON6 0.6 4 180.0 !
+ON5 CN7 CN7 ON6 0.2 3 0.0 !
+ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA
+ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA
+ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA
+ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo
+
+!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1'
+! This term can be used to adjust the c2'endo/c3'endo
+! energy difference in THF5P
+CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80]
+CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA
+CN7B ON6B CN7 CN9 2.0 3 0.0 ! To lower barrier in RNA, 5MET
+!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1'
+! This term can be used to adjust the c2'endo/c3'endo
+! When O3' is ON2
+ON2 CN7 CN8 CN7B 0.8 6 0.0 !
+ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right
+ON2 CN7 CN8 CN7B 2.0 3 180.0 !
+ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA
+ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA
+ON2 CN7 CN7B CN7B 1.6 3 180.0 !
+!When O3' is ON5 (patch 3TER)
+ON5 CN7 CN8 CN7B 0.8 6 0.0 !
+ON5 CN7 CN8 CN7B 0.4 5 0.0 !
+ON5 CN7 CN8 CN7B 2.0 3 180.0 !
+ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo
+ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA
+ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA
+!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H
+ON2 CN7 CN8 HN8 0.195 3 0.0 !
+ON5 CN7 CN8 HN8 0.195 3 180.0 !
+ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA
+ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA
+!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3'
+HN7 CN7 CN7 ON2 0.195 3 0.0
+HN7 CN7 CN7 ON5 0.195 3 0.0
+!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P
+CN7 CN7 ON2 P2 0.6 5 0.0 !eps, adm, 2011 DNA update
+CN7 CN7 ON2 P2 0.2 4 0.0 !eps, locat of 200 mimima, adm, 2011 DNA update
+CN7 CN7 ON2 P2 0.0 3 180.0 !eps, barE beteen minima, adm, 2011 DNA update
+CN7 CN7 ON2 P2 0.4 2 0.0 !eps, relE of 200 vs 275 min, adm, 2011 DNA update
+CN7 CN7 ON2 P2 1.9 1 180.0 !eps, adm, 2011 DNA update
+CN7 CN7 ON2 P 0.6 5 0.0 !eps, RNA
+CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima, RNA
+CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima, RNA
+CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min, RNA
+CN7 CN7 ON2 P 1.9 1 180.0 !eps, RNA
+!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P
+! This term is involved in epsilon
+CN8 CN7 ON2 P 2.5 1 180.0 ! 3-terminal phosphate
+CN8 CN7 ON2 P2 1.9 1 180.0 ! adm, 2011 DNA update new param, eps
+CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA
+CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
+CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
+! base on thfalloh
+! the following differ significantly from the protein based
+! alcohol parameters (based on ethanol, see above)
+CN7 CN7 ON5 HN5 0.5 3 0.0
+CN7 CN7 ON5 HN5 0.3 2 180.0
+CN7 CN7 ON5 HN5 1.5 1 0.0
+CN8 CN7 ON5 HN5 0.5 3 0.0
+CN8 CN7 ON5 HN5 1.0 2 180.0
+CN8 CN7 ON5 HN5 0.3 1 0.0
+CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA
+CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA
+! Was simply transfered from HN7 CN7 ON2 P
+! adm jr. should convert to alcohol term (see ribose etc)
+HN7 CN7 ON5 HN5 0.0 3 0.0
+HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H
+HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5'
+!@@@@@@ End of torsions involving exocyclic atoms:
+!@@@@@@ Begining of torsions for endocyclic atoms only:
+CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4'
+CN8 CN7 CN7 ON6 1.0 4 0.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; lowers c3'endo
+CN8 CN7 CN7 ON6 0.3 5 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
+CN8 CN7 CN7 ON6 0.3 6 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
+CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier
+CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA
+!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
+!======== CN7 CN8 CN8 ON6 from thfoh ==============================
+CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier
+CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA
+!======== C1'-C2'-C3'-C4' ========
+CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes
+CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA
+!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
+!======== CN7 CN7 ON6 CN8 from thfohch3 ============================
+CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1'
+CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA
+!======== Directly adjusted with TM3P
+HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5'
+!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
+HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
+HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3'
+HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful
+HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4'
+HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H
+HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H
+HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H
+HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc*
+HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
+HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4'
+HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA
+HN9 CN9 CN7 ON6B 0.195 3 180.0 ! RNA, 5MET
+HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA
+HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA
+HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA
+HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1'
+HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3'
+HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4'
+!@@@@@@ End of torsions for endocyclic atoms only
+
+!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@
+! N9-C1'-C2'-O2':
+NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine
+NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil
+ON5 CN7B CN7B HN7 0.000 3 0.0 !
+HN7 CN7B CN7B HN7 0.000 3 0.0 !
+CN7 CN7 CN7B ON5 0.000 3 0.0
+ON6B CN7B CN7B ON5 0.000 3 0.0
+ON5 CN7B CN7 ON2 0.000 3 0.0
+! for ndph
+ON5 CN7 CN7B ON2 0.000 3 0.0
+ON5 CN7B CN7 ON5 0.000 3 0.0
+HN7 CN7B ON5 HN5 0.000 3 0.0
+!ejd, 2010 RNA update
+HN5 ON5 CN7B CN7B 0.000 6 180.0 ! ejd, 2010 RNA update
+HN5 ON5 CN7B CN7B 0.400 3 0.0 ! shifts min, ejd, 2010 RNA update
+HN5 ON5 CN7B CN7B 0.400 2 0.0 ! ejd, 2010 RNA update
+HN5 ON5 CN7B CN7B 0.800 1 0.0 ! height of right barrier and can shift min, ejd, 2010 RNA update
+!to C3'
+HN5 ON5 CN7B CN7 0.200 3 0.0 ! ejd, 2010 RNA update
+HN5 ON5 CN7B CN7 0.000 2 180.0 ! ejd, 2010 RNA update
+HN5 ON5 CN7B CN7 2.000 1 0.0 ! height of left side barrier, ejd, 2010 RNA update
+!@@@@@@ End of torsions specifically defined for RNA @@@@@@
+
+!Collection of parameters that were previously incorrectly categorized or labeled
+CN7B ON6 CN7 CN9 0.0 3 0.0 ! added for sugar model compounds
+HN7 CN7 CN7B ON5 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7 CN7B CN7 CN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7 CN7 CN7 CN7B 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
+HN7 CN7 CN7B HN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+!
+HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97
+NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97
+HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97
+NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97
+CN1 X X ON1 90.0 0 0.0 !U
+CN1T X X ON1 90.0 0 0.0 !U
+CN1 NN2G CN5G ON1 90.0 0 0.0 !G
+CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97
+CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97
+CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91
+CN2 X X NN1 90.0 0 0.0 !C,
+CN2 NN3G NN2G NN1 40.0 0 0.0 !G
+CN2 NN3A CN5 NN1 40.0 0 0.0 !A
+CN2 NN3 CN3 NN1 60.0 0 0.0 !C,
+CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97
+
+! Wildcards used to minimize memory requirements
+NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
+ CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
+!
+HN1 0.0 -0.0460 0.2245
+HN2 0.0 -0.0460 0.2245
+HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw
+HN4 0.0 -0.0460 0.2245
+HN5 0.0 -0.0460 0.2245
+HN6 0.0 -0.0220 1.3200
+HN7 0.0 -0.0220 1.3200
+HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8
+HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9
+!
+NN1 0.0 -0.20 1.85
+NN2 0.0 -0.20 1.85
+NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines
+NN2G 0.0 -0.20 1.85
+NN2U 0.0 -0.20 1.85
+NN3 0.0 -0.20 1.85
+NN3A 0.0 -0.20 1.85
+NN3G 0.0 -0.20 1.85
+NN4 0.0 -0.20 1.85
+NN6 0.0 -0.20 1.85
+!
+ON1 0.0 -0.1200 1.70
+ON1C 0.0 -0.1200 1.70
+ON2 0.0 -0.1521 1.77
+ON3 0.0 -0.1200 1.70
+ON4 0.0 -0.1521 1.77
+ON5 0.0 -0.1521 1.77
+ON6 0.0 -0.1521 1.77
+ON6B 0.0 -0.1521 1.77
+!
+! base ring C vdw param, 11/14/97, adm jr
+CN1 0.0 -0.10 1.9000
+CN1T 0.0 -0.10 1.9000
+CN2 0.0 -0.10 1.9000
+CN3 0.0 -0.09 1.9000
+CN3T 0.0 -0.09 1.9000 ! T, adm jr.
+CN4 0.0 -0.075 1.9000
+CN5 0.0 -0.075 1.9000
+CN5G 0.0 -0.075 1.9000
+CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
+CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
+! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
+CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
+CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
+CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 !
+!
+P 0.0 -0.585 2.15
+P2 0.0 -0.585 2.15
+
+NBFIX
+! Emin Rmin
+! (kcal/mol) (A)
+!
+
+HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
+ ! READ PARAM APPEND CARD
+ ! to append hbond parameters from the file: par_hbond.inp
+
+END
diff --git a/arbdmodel/resources/charmm36.nbfix/par_water_ions_na.prm b/arbdmodel/resources/charmm36.nbfix/par_water_ions_na.prm
new file mode 100644
index 0000000000000000000000000000000000000000..f76ef92ae3322466f5d6268923a234d39d73602c
--- /dev/null
+++ b/arbdmodel/resources/charmm36.nbfix/par_water_ions_na.prm
@@ -0,0 +1,203 @@
+
+!read para card flex @app
+!* Parameters for water and ions
+!*
+
+!ATOMS
+!MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN
+!MASS 2 HX 1.00800 ! hydroxide hydrogen
+!MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN
+!MASS 4 OX 15.99940 ! hydroxide oxygen
+!MASS 5 LIT 6.94100 ! Lithium ion
+!MASS 6 SOD 22.98977 ! Sodium Ion
+!MASS 7 MG 24.30500 ! Magnesium Ion
+!MASS 8 POT 39.09830 ! Potassium Ion
+!MASS 9 CAL 40.08000 ! Calcium Ion
+!MASS 10 RUB 85.46780 ! Rubidium Ion
+!MASS 11 CES 132.90545 ! Cesium Ion
+!MASS 12 BAR 137.32700 ! Barium Ion
+!MASS 13 ZN 65.37000 ! zinc (II) cation
+!MASS 14 CAD 112.41100 ! cadmium (II) cation
+!MASS 15 CLA 35.45000 ! Chloride Ion
+!MASS 16 OTMG 15.99940 ! TIPS3P WATER OXYGEN by jejoong
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
+HT OT 450.0 0.9572 ! from TIPS3P geometry
+OX HX 545.0 0.9700 ! hydroxide ion
+!jejoong
+MG OTMG 10000.00 1.9400 !
+OTMG HT 450.000 0.9572
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types Ktheta Theta0 Kub S0
+!
+HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
+!jejoong
+HT OTMG HT 55.000 104.5200
+HT OTMG MG 0.000 104.5200
+OTMG MG OTMG 1000.000 90.0000
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+HT OTMG MG OTMG 0.000 6 180.0000
+
+
+!
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+
+NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+
+!TIP3P LJ parameters
+HT 0.0 -0.046 0.2245
+OT 0.0 -0.1521 1.7682
+!jejoong
+OTMG 0.000000 -0.152100 1.768200 ! TIP3P oxygen
+
+!for hydroxide
+OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION
+ ! JG 8/27/89
+HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
+ ! same as TIP3P hydrogen, adm jr., 7/20/89
+
+!ions
+LIT 0.0 -0.00233 1.2975 ! Lithium
+ ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006)
+SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium
+ ! ddG of -18.6 kcal/mol with K+ from S. Noskov
+MG 0.0 -0.0150 1.18500 ! Magnesium
+ ! B. Roux dA = -441.65
+POT 0.0 -0.0870 1.76375 ! Potassium
+ ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
+CAL 0.0 -0.120 1.367 ! Calcium
+ ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
+RUB 0.0000 -0.15 1.90 ! Rubidium
+ ! delta A with respect to POT is +6.0 kcal/mol in bulk water
+CES 0.0 -0.1900 2.100 ! Cesium
+ ! delta A with respect to POT is +12.0 kcal/mol
+BAR 0.0 -0.150 1.890 ! Barium
+ ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol
+ZN 0.000000 -0.250000 1.090000 ! Zinc
+ ! RHS March 18, 1990
+CAD 0.000000 -0.120000 1.357000 ! Cadmium
+ ! S. Marchand and B. Roux, from delta delta G
+CLA 0.0 -0.150 2.27 ! Chloride
+ ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
+
+NBFIX
+! Emin Rmin
+! (kcal/mol) (A)
+!SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
+!POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
+! monovalent cation -- protein acetate (OC), lipid acetate (OCL)
+!LIT OC -0.016721 2.9975 ! standard
+!LIT OC -0.016721 3.1875 ! +0.19
+!LIT OCL -0.016721 3.1875 ! +0.19
+!SOD OC -0.075020 3.11075 ! standard
+!SOD OC -0.075020 3.20075 ! +0.09
+!SOD OCL -0.075020 3.20075 ! +0.09
+!POT OC -0.102176 3.46375 ! standard
+!POT OC -0.102176 3.54375 ! +0.08
+!POT OCL -0.102176 3.54375 ! +0.08
+! monovalent cation -- lipid phosphate (O2L), nucleic acid phosphate (ON3)
+!LIT OC -0.016721 2.9975 ! standard
+!LIT O2L -0.016721 3.1875 ! +0.19
+ LIT ON3 -0.016721 3.1875 ! +0.19
+!SOD OC -0.075020 3.11075 ! standard
+!SOD O2L -0.075020 3.20075 ! +0.09
+ SOD ON3 -0.075020 3.20075 ! +0.09
+!POT OC -0.102176 3.46375 ! standard
+!POT O2L -0.102176 3.54375 ! +0.08
+ POT ON3 -0.102176 3.54375 ! +0.08
+! monovalent cation -- chloride
+!LIT CLA -0.018695 3.5675 ! standard
+ LIT CLA -0.018695 3.7975 ! +0.23
+!SOD CLA -0.083875 3.68075 ! standard
+ SOD CLA -0.083875 3.74075 ! +0.06
+!POT CLA -0.114237 4.03375 ! standard
+ POT CLA -0.114237 4.08375 ! +0.05
+! magnesium -- chloride
+!OTMG CLA -0.151046 4.03820 ! standard
+ OTMG CLA -0.151046 4.05320 ! +0.015
+! magnesium -- acetate / phosphate
+!OTMG OC -0.135099 3.46820 ! standard
+!OTMG OC -0.135099 3.52320 ! +0.055
+!OTMG OCL -0.135099 3.52320 ! +0.055
+!OTMG O2L -0.135099 3.52320 ! +0.055
+ OTMG ON3 -0.135099 3.52320 ! +0.055
+
+END
+
+! The following section contains NBFixes for sodium interacting with
+! carboxylate oxygens of various CHARMM force fields. It will generate
+! level -1 warnings whenever any of these force fields have not been
+! read prior to the current stream file. Since we don't want to force
+! the user to always read all the force fields, we're suppressing the
+! warnings. The only side effect is that you will have "most severe
+! warning was at level 0" at the end of your output. Also note that
+! the user is responsible for reading the current file last if they
+! want the NBFixes to apply. A more elegant solution would require new
+! features to be added to CHARMM.
+! parallel fix, to avoid duplicated messages in the log
+!set para
+!if ?NUMNODE gt 1 set para node 0
+
+!set wrn ?WRNLEV
+! Some versions of CHARMM don't seem to initialize wrnlev...
+!if "@WRN" eq "?WRNLEV" set wrn 5
+!set bom ?bomlev
+!WRNLEV -1 @PARA
+!BOMLEV -1 @PARA
+!!read para card flex append
+!* NBFix between carboxylate and sodium
+!*
+
+! These NBFixes will only apply if the main files have been read in first!!!
+!NBFIX
+!SOD OC -0.075020 3.190 ! For prot carboxylate groups
+!SOD OCL -0.075020 3.190 ! For lipid carboxylate groups
+!SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups
+!SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups
+
+!END
+!BOMLEV @bom @PARA
+!WRNLEV @wrn @PARA
+
+return
+
diff --git a/arbdmodel/resources/charmm36.nbfix/top_all36_na.rtf b/arbdmodel/resources/charmm36.nbfix/top_all36_na.rtf
new file mode 100644
index 0000000000000000000000000000000000000000..04cd970835a0493fbdd64bb21bbd90368681ab15
--- /dev/null
+++ b/arbdmodel/resources/charmm36.nbfix/top_all36_na.rtf
@@ -0,0 +1,853 @@
+* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ////
+* Alexander D. MacKerell Jr. and coworkers
+* April 2011
+* All comments to the CHARMM web site: www.charmm.org
+* parameter set discussion forum
+*
+36 1
+
+!2010/2011 additions
+! ejd, 2010 RNA update
+! adm, 2011 DNA update
+! For DNA update, new atom type required for P of DNA. This required
+! replication of a number of parameters and the creation of new
+! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
+! CHARMM scripts to generate DNA will no longer work. Note that the
+! atom type change to P3 ONLY applies to the phosphodester linkage in
+! DNA and NOT to terminal phosphates, DMP etc.
+!
+
+!example of new generate/patch combination to generate DNA
+!
+!read sequence card
+!* 1bna, strand 1
+!*
+!3
+!cyt gua cyt
+!
+!generate a first 5ter last 3ter setup warn
+!
+!patch deo5 a 1 setup warn !special patch for 5-terminal deoxy residue
+!patch deox a 2 setup warn !new patch to convert RNA to DNA
+!patch deox a 3 setup warn !no special patch required for 3-terminal deoxy residue
+!
+!autogenerate angles dihedrals !Use of AUTOGENERATE is essential
+
+!
+!references
+!
+!NUCLEIC ACIDS
+!
+!Hart, Baker, Nilsson and MacKerell, DNA BI/BII equilibrium, in progress
+!
+!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
+!“Impact of 2’-hydroxyl sampling on the conformational properties of
+!RNA: Update of the CHARMM all-atom additive force field for RNA,â€
+!JCC, In Press, 2011, NIHMSID #272247
+
+!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
+!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
+!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
+!
+!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
+!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
+!and RNA in Solution. JCC, 2000, 21: 105-120.
+!
+
+
+MASS 91 HN1 1.008000 H ! Nucleic acid amine proton
+MASS 92 HN2 1.008000 H ! Nucleic acid ring nitrogen proton
+MASS 93 HN3 1.008000 H ! Nucleic acid aromatic carbon proton
+MASS 94 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton
+MASS 95 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton
+MASS 96 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton
+MASS 97 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA)
+MASS 98 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds
+MASS 99 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds
+MASS 100 CN1 12.011000 C ! Nucleic acid carbonyl carbon
+MASS 101 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2)
+MASS 102 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide
+MASS 103 CN3 12.011000 C ! Nucleic acid aromatic carbon
+MASS 104 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
+MASS 105 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2
+MASS 106 CN5 12.011000 C ! Nucleic acid purine C4 and C5
+MASS 107 CN5G 12.011000 C ! Nucleic acid guanine C5
+MASS 108 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
+MASS 109 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'
+MASS 110 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
+MASS 111 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
+MASS 112 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
+MASS 113 NN1 14.007000 N ! Nucleic acid amide nitrogen
+MASS 114 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen
+MASS 115 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE
+MASS 116 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
+MASS 117 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
+MASS 118 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen
+MASS 119 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
+MASS 120 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3
+MASS 121 NN4 14.007000 N ! Nucleic acid purine N7
+MASS 122 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
+MASS 123 ON1 15.999400 O ! Nucleic acid carbonyl oxygen
+MASS 124 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
+MASS 125 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen
+MASS 126 ON3 15.999400 O ! Nucleic acid =O in phosphate
+MASS 127 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
+MASS 128 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen
+MASS 129 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen
+MASS 130 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen
+MASS 131 P 30.974000 P ! phosphorus
+MASS 132 P2 30.974000 P ! phosphorus, adm, 2011 DNA update
+
+DECL +P
+DECL +O1P
+DECL +O2P
+DECL +O5'
+DECL -O3'
+
+DEFA FIRS none LAST none
+AUTOGENERATE ANGLES DIHEDRALS PATCH
+
+RESI GUA -1.00 ! O6
+ATOM P P 1.50 ! ||
+ATOM O1P ON3 -0.78 ! C6
+ATOM O2P ON3 -0.78 ! / \
+ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\
+ATOM C5' CN8B -0.08 ! | || C8-H8
+ATOM H5' HN8 0.09 ! C2 C4--N9/
+ATOM H5'' HN8 0.09 ! / \\ / \
+GROUP ! H21-N2 N3 \
+ATOM C4' CN7 0.16 ! | \
+ATOM H4' HN7 0.09 ! H22 \
+ATOM O4' ON6B -0.50 ! \
+ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
+ATOM H1' HN7 0.09 ! | | \ / \ \
+GROUP ! -P-O5'-C5'---C4' C1'
+ATOM N9 NN2B -0.02 ! | | \ / \
+ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1'
+ATOM N2 NN1 -0.68 ! / \ / \
+ATOM H21 HN1 0.32 ! O3' H3' O2' H2''
+ATOM H22 HN1 0.35 ! | |
+ATOM N3 NN3G -0.74 ! H2'
+ATOM C2 CN2 0.75
+ATOM N1 NN2G -0.34
+ATOM H1 HN2 0.26
+ATOM C6 CN1 0.54
+ATOM O6 ON1 -0.51
+ATOM C5 CN5G 0.00
+ATOM N7 NN4 -0.60
+ATOM C8 CN4 0.25
+ATOM H8 HN3 0.16
+GROUP
+ATOM C2' CN7B 0.14
+ATOM H2'' HN7 0.09
+ATOM O2' ON5 -0.66
+ATOM H2' HN5 0.43
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM O3' ON2 -0.57
+BOND P O1P P O2P P O5'
+BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
+BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
+BOND C2 N2 C2 N1 N2 H21
+BOND N2 H22 N1 H1 N1 C6 C6 C5
+BOND C5 N7 C2' C3' C3' O3' O3' +P
+BOND C2' O2' O2' H2'
+BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
+BOND C5' H5'' C8 H8
+DOUBLE C2 N3 C4 C5 N7 C8 C6 O6
+IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
+DONO H21 N2
+DONO H22 N2
+DONO H1 N1
+DONO H2' O2'
+ACCE O6 C6
+ACCE N3
+ACCE N7
+ACCE O1P P
+ACCE O2P P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+! Chi and sugar-phosphate backbone in B-DNA like conformation
+BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
+BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
+BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
+BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
+BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
+BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
+BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
+BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
+BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
+BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
+BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
+BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
+BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
+BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
+BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
+BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
+BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
+BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
+BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
+BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
+BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
+BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
+BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
+BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
+BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
+BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
+BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
+BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
+BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
+BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
+BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
+
+
+RESI ADE -1.00 ! H61 H62!
+ATOM P P 1.50 ! \ /
+ATOM O1P ON3 -0.78 ! N6
+ATOM O2P ON3 -0.78 ! |
+ATOM O5' ON2 -0.57 ! C6
+ATOM C5' CN8B -0.08 ! // \
+ATOM H5' HN8 0.09 ! N1 C5--N7\\
+ATOM H5'' HN8 0.09 ! | || C8-H8
+GROUP ! C2 C4--N9/
+ATOM C4' CN7 0.16 ! / \\ / \
+ATOM H4' HN7 0.09 ! H2 N3 \
+ATOM O4' ON6B -0.50 ! \
+ATOM C1' CN7B 0.16 ! \
+ATOM H1' HN7 0.09 ! \
+GROUP ! O1P H5' H4' O4' \
+ATOM N9 NN2 -0.05 ! | | \ / \ \
+ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1'
+ATOM N7 NN4 -0.71 ! | | \ / \
+ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1'
+ATOM H8 HN3 0.12 ! / \ / \
+ATOM N1 NN3A -0.74 ! O3' H3' O2' H2''
+ATOM C2 CN4 0.50 ! | |
+ATOM H2 HN3 0.13 ! H2'
+ATOM N3 NN3A -0.75
+ATOM C4 CN5 0.43
+ATOM C6 CN2 0.46
+ATOM N6 NN1 -0.77
+ATOM H61 HN1 0.38
+ATOM H62 HN1 0.38
+GROUP
+ATOM C2' CN7B 0.14
+ATOM H2'' HN7 0.09
+ATOM O2' ON5 -0.66
+ATOM H2' HN5 0.43
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM O3' ON2 -0.57
+BOND P O1P P O2P P O5'
+BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
+BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
+BOND C2 N1 C6 N6
+BOND N6 H61 N6 H62 C6 C5 C5 N7
+BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P
+BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
+BOND C5' H5'' C8 H8 C2 H2
+DOUBLE N1 C6 C2 N3 C4 C5 N7 C8
+IMPR N6 C6 H61 H62 C6 N1 C5 N6
+DONO H61 N6
+DONO H62 N6
+DONO H2' O2'
+ACCE N3
+ACCE N7
+ACCE N1
+ACCE O1P P
+ACCE O2P P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
+BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
+BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
+BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
+BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
+BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
+BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
+BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
+BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
+BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
+BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
+BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
+BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
+BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
+BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
+BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
+BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
+BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
+BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
+BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
+BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
+BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
+BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
+BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
+BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
+BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
+BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
+BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
+BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
+BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
+BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
+BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
+BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
+
+RESI CYT -1.00
+ATOM P P 1.50 !
+ATOM O1P ON3 -0.78 ! H42 H41
+ATOM O2P ON3 -0.78 ! \ /
+ATOM O5' ON2 -0.57 ! N4
+ATOM C5' CN8B -0.08 ! |
+ATOM H5' HN8 0.09 ! C4
+ATOM H5'' HN8 0.09 ! / \\
+GROUP ! H5-C5 N3
+ATOM C4' CN7 0.16 ! || |
+ATOM H4' HN7 0.09 ! H6-C6 C2
+ATOM O4' ON6B -0.50 ! \ / \\
+ATOM C1' CN7B 0.16 ! N1 O2
+ATOM H1' HN7 0.09 ! \
+GROUP ! \
+ATOM N1 NN2 -0.13 ! \
+ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \
+ATOM H6 HN3 0.17 ! | | \ / \ \
+ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1'
+ATOM H5 HN3 0.07 ! | | \ / \
+ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1'
+ATOM O2 ON1C -0.49 ! / \ / \
+ATOM N3 NN3 -0.66 ! O3' H3' O2' H2''
+ATOM C4 CN2 0.65 ! | |
+ATOM N4 NN1 -0.75 ! H2'
+ATOM H41 HN1 0.37
+ATOM H42 HN1 0.33
+GROUP
+ATOM C2' CN7B 0.14
+ATOM H2'' HN7 0.09
+ATOM O2' ON5 -0.66
+ATOM H2' HN5 0.43
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM O3' ON2 -0.57
+BOND P O1P P O2P P O5'
+BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
+BOND C1' N1 C1' C2' N1 C2 N1 C6
+BOND C2 N3 C4 N4 N4 H41 N4 H42
+BOND C4 C5 C2' C3' C3' O3' O3' +P
+BOND C2' O2' O2' H2'
+BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
+BOND C5' H5'' C5 H5 C6 H6
+DOUBLE C2 O2 C5 C6 N3 C4
+IMPR C2 N1 N3 O2 C4 N3 C5 N4
+IMPR N4 C4 H41 H42
+DONO H42 N4
+DONO H2' O2'
+DONO H41 N4
+ACCE O2 C2
+ACCE N3
+ACCE O1P P
+ACCE O2P P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
+BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
+BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
+BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
+BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
+BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
+BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
+BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
+BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
+BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
+BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
+BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
+BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
+BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
+BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
+BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
+BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
+BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
+BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
+BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
+BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
+BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
+BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
+BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
+BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
+BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
+BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
+BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
+
+RESI THY -1.00 ! H51 O4
+ATOM P P 1.50 ! | ||
+ATOM O1P ON3 -0.78 ! H52-C5M C4 H3
+ATOM O2P ON3 -0.78 ! | \ / \ /
+ATOM O5' ON2 -0.57 ! H53 C5 N3
+ATOM C5' CN8B -0.08 ! || |
+ATOM H5' HN8 0.09 ! H6-C6 C2
+ATOM H5'' HN8 0.09 ! \ / \\
+GROUP ! N1 O2
+ATOM C4' CN7 0.16 ! \
+ATOM H4' HN7 0.09 ! \
+ATOM O4' ON6B -0.50 ! \
+ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
+ATOM H1' HN7 0.09 ! | | \ / \ \
+GROUP ! -P-O5'-C5'---C4' C1'
+ATOM N1 NN2B -0.34 ! | | \ / \
+ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1'
+ATOM H6 HN3 0.17 ! / \ / \
+ATOM C2 CN1T 0.51 ! O3' H3' O2' H2''
+ATOM O2 ON1 -0.41 ! | |
+ATOM N3 NN2U -0.46 ! H2'
+ATOM H3 HN2 0.36 !
+ATOM C4 CN1 0.50 !
+ATOM O4 ON1 -0.45 !
+ATOM C5 CN3T -0.15
+ATOM C5M CN9 -0.11
+ATOM H51 HN9 0.07
+ATOM H52 HN9 0.07
+ATOM H53 HN9 0.07
+GROUP
+ATOM C2' CN7B 0.14
+ATOM H2'' HN7 0.09
+ATOM O2' ON5 -0.66
+ATOM H2' HN5 0.43
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM O3' ON2 -0.57
+BOND P O1P P O2P P O5'
+BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
+BOND C1' N1 C1' C2' N1 C2 N1 C6
+BOND C2 N3 N3 H3 N3 C4 C4 C5
+BOND C5 C5M C2' C3' C3' O3' O3' +P
+BOND C2' O2' O2' H2'
+BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
+BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53
+DOUBLE C2 O2 C4 O4 C5 C6
+IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
+DONO H3 N3
+DONO H2' O2'
+ACCE O2 C2
+ACCE O4 C4
+ACCE O1P P
+ACCE O2P P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+
+BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
+BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
+BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
+BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
+BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
+BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
+BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
+BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
+BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
+BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
+BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
+BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
+BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
+BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
+BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
+BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
+BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
+BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
+BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
+BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
+BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
+BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
+BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
+BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
+BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
+BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
+BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
+BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
+BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
+
+RESI URA -1.00 ! O4
+ATOM P P 1.50 ! ||
+ATOM O1P ON3 -0.78 ! C4 H3
+ATOM O2P ON3 -0.78 ! / \ /
+ATOM O5' ON2 -0.57 ! H5-C5 N3
+ATOM C5' CN8B -0.08 ! || |
+ATOM H5' HN8 0.09 ! H6-C6 C2
+ATOM H5'' HN8 0.09 ! \ / \\
+GROUP ! N1 O2
+ATOM C4' CN7 0.16 ! \
+ATOM H4' HN7 0.09 ! \
+ATOM O4' ON6B -0.50 ! \
+ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
+ATOM H1' HN7 0.09 ! | | \ / \ \
+GROUP ! -P-O5'-C5'---C4' C1'
+ATOM N1 NN2B -0.34 ! | | \ / \
+ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1'
+ATOM H6 HN3 0.14 ! / \ / \
+ATOM C2 CN1T 0.55 ! O3' H3' O2' H2''
+ATOM O2 ON1 -0.45 ! | |
+ATOM N3 NN2U -0.46 ! H2'
+ATOM H3 HN2 0.36 !
+ATOM C4 CN1 0.53 !
+ATOM O4 ON1 -0.48 !
+ATOM C5 CN3 -0.15 !
+ATOM H5 HN3 0.10 !
+GROUP
+ATOM C2' CN7B 0.14
+ATOM H2'' HN7 0.09
+ATOM O2' ON5 -0.66
+ATOM H2' HN5 0.43
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM O3' ON2 -0.57
+BOND P O1P P O2P P O5'
+BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
+BOND C1' N1 C1' C2' N1 C2 N1 C6
+BOND C2 N3 N3 H3 N3 C4 C4 C5
+BOND C2' C3' C3' O3' O3' +P
+BOND C2' O2' O2' H2'
+BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
+BOND C5' H5'' C5 H5 C6 H6
+DOUBLE C2 O2 C4 O4 C5 C6
+IMPR C2 N1 N3 O2 C4 N3 C5 O4
+DONO H3 N3
+DONO H2' O2'
+ACCE O2 C2
+ACCE O4 C4
+ACCE O1P P
+ACCE O2P P
+ACCE O2'
+ACCE O3'
+ACCE O4'
+ACCE O5'
+BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
+BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
+BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
+BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
+BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
+BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
+BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
+BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
+BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
+BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
+BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
+BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
+BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
+BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
+BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
+BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
+BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
+BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
+BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
+BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
+BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
+BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
+BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
+BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
+BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
+BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
+BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
+BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
+BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
+
+! NOTE the option to regenerate all angles and dihedrals allows
+! the explicit inclusion of the THET and DIHE terms to be omitted
+! even if the PRES is used in a PATCH statement. It is important to
+! inspect the patches prior to use to determine if they should be used
+! in a GENErate or PATCh statement and/or if the AUTOgeneration of
+! angles and dihedrals is required.
+! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
+! documentation
+
+PRES DEO5 0.00 ! Patch to make the 5-terminal nucleotide into DEOXYribose
+DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS
+
+GROUP ! To correct O4' atom type in DNA (NF)
+ATOM C4' CN7 0.16 !
+ATOM H4' HN7 0.09 !
+ATOM O4' ON6 -0.50 !
+ATOM C1' CN7B 0.16 !
+ATOM H1' HN7 0.09 !
+GROUP
+ATOM C2' CN8 -0.18
+ATOM H2' HN8 0.09
+ATOM H2'' HN8 0.09
+
+BOND C2' H2'
+BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
+
+PRES DEOX 1.50 ! Patch to make non 5-terminal DEOXyribose nucleotides
+DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS
+
+ATOM P P2 1.50 ! switch type P to type P2 as required to apply
+ ! 2011 DNA update to zeta in DNA only
+GROUP ! To correct O4' atom type in DNA (NF)
+ATOM C4' CN7 0.16 !
+ATOM H4' HN7 0.09 !
+ATOM O4' ON6 -0.50 !
+ATOM C1' CN7B 0.16 !
+ATOM H1' HN7 0.09 !
+GROUP
+ATOM C2' CN8 -0.18
+ATOM H2' HN8 0.09
+ATOM H2'' HN8 0.09
+
+BOND C2' H2'
+BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
+
+PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH
+ ! use in generate statement
+GROUP
+ATOM H5T HN5 0.43
+ATOM O5' ON5 -0.66
+ATOM C5' CN8B 0.05
+ATOM H5' HN8 0.09
+ATOM H5'' HN8 0.09
+!
+DELETE ATOM P
+DELETE ATOM O1P
+DELETE ATOM O2P
+!
+BOND H5T O5'
+DONO H5T O5'
+BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000
+
+PRES 5MET 0.00 ! 5'-ribose METHYL patch
+ ! use in generate statement, doesn't work with DEOx patches
+GROUP
+ATOM C5' CN9 -0.27
+ATOM H5' HN9 0.09
+ATOM H5'' HN9 0.09
+ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY
+!
+DELETE ATOM O5'
+DELETE ATOM P
+DELETE ATOM O1P
+DELETE ATOM O2P
+!
+BOND C5' H53'
+IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000
+IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000
+IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000
+
+PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch
+ ! use in generate statement
+GROUP
+ATOM C5' CN8B -0.08
+ATOM H5' HN8 0.09
+ATOM H5'' HN8 0.09
+ATOM P P 1.50
+ATOM O1P ON3 -0.82
+ATOM O2P ON3 -0.82
+ATOM O5' ON2 -0.62
+ATOM O5T ON4 -0.68
+ATOM H5T HN4 0.34
+BOND O5T P H5T O5T
+DONO H5T O5T
+! Built in B-DNA-like conformation (NF)
+BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
+BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
+BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
+BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
+BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
+
+PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch
+ ! use in generate statement
+GROUP
+ATOM C5' CN8B -0.08
+ATOM H5' HN8 0.09
+ATOM H5'' HN8 0.09
+ATOM P P 1.50
+ATOM O1P ON3 -0.78
+ATOM O2P ON3 -0.78
+ATOM O5' ON2 -0.57
+ATOM O5T ON2 -0.57
+ATOM C5T CN9 -0.17
+ATOM H5T1 HN9 0.09
+ATOM H5T2 HN9 0.09
+ATOM H5T3 HN9 0.09
+
+BOND O5T P O5T C5T C5T H5T1 C5T H5T2
+BOND C5T H5T3
+!DONO H5T O5T
+! Built in B-DNA-like conformation (NF)
+BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
+BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
+BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
+BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
+BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
+BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000
+BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000
+BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000
+
+PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH
+ ! use in generate statement
+GROUP
+ATOM C3' CN7 0.14
+ATOM H3' HN7 0.09
+ATOM O3' ON5 -0.66
+ATOM H3T HN5 0.43
+BOND O3' H3T
+DONO H3T O3'
+BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284
+
+PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch
+ ! use in generate statement
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM P3 P 1.50
+ATOM O1P3 ON3 -0.82
+ATOM O2P3 ON3 -0.82
+ATOM O3' ON2 -0.62
+ATOM O3T ON4 -0.68
+ATOM H3T HN4 0.34
+BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T
+DONO H3T O3T
+ACCE O3T
+ACCE O1P3
+ACCE O2P3
+! Build in B-DNA-like conformation (NF)
+BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
+BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000
+BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
+BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
+BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
+
+PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch
+ ! use in generate statement
+! To build model compound with OPO3-CH3 at the 3' end (nicolas)
+GROUP
+ATOM C3' CN7 0.01
+ATOM H3' HN7 0.09
+ATOM P3 P 1.50
+ATOM O1P3 ON3 -0.78
+ATOM O2P3 ON3 -0.78
+ATOM O3' ON2 -0.57
+ATOM O3T ON2 -0.57
+ATOM C3T CN9 -0.17
+ATOM H3T1 HN9 0.09
+ATOM H3T2 HN9 0.09
+ATOM H3T3 HN9 0.09
+
+BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T
+BOND C3T H3T1 C3T H3T2 C3T H3T3
+ACCE O3'
+ACCE O5'
+ACCE O1P3
+ACCE O2P3
+BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
+BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000
+BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
+BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
+BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
+BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000
+BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000
+BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000
+
+PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch
+ ! use in generate statement
+ ! Added by Nicolas, to be consistent with model componds
+GROUP
+ATOM C3' CN7 -0.09
+ATOM H3' HN7 0.09
+ATOM P3 P 1.10
+ATOM O3' ON2 -0.40
+ATOM O1P3 ON3 -0.90
+ATOM O2P3 ON3 -0.90
+ATOM O3P3 ON3 -0.90
+BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3
+ACCE O1P3
+ACCE O2P3
+ACCE O3P3
+BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000
+BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000
+BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
+BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
+BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000
+BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000
+
+PRES DELB 0.00 ! patch to delete all possible base atoms
+ ! of Cyt,Gua,Ade,Thy and Ura
+ !
+!note: error messages will be obtained due to atoms not present in
+!residue being "deleted" by this patch
+!cyt section
+DELE ATOM N1
+DELE ATOM C6
+DELE ATOM H6
+DELE ATOM C2
+DELE ATOM O2
+DELE ATOM N3
+DELE ATOM C4
+DELE ATOM N4
+DELE ATOM H41
+DELE ATOM H42
+DELE ATOM C5
+DELE ATOM H5
+!gua section
+DELE ATOM N9
+DELE ATOM H1
+DELE ATOM N2
+DELE ATOM H21
+DELE ATOM H22
+DELE ATOM O6
+DELE ATOM N7
+DELE ATOM C8
+DELE ATOM H8
+!ade section
+DELE ATOM H2
+DELE ATOM N6
+DELE ATOM H61
+DELE ATOM H62
+!thy/ura section
+DELE ATOM H3
+DELE ATOM O4
+DELE ATOM C5M
+DELE ATOM H51
+DELE ATOM H52
+DELE ATOM H53
+
+PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide
+ ! use AUTOGEN ANGLE DIHE after this patch
+BOND O3' P ! but before water-generation
+
+PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES)
+ ! eg: patch sega 10 segb 1
+ ! sega should have std 3' (gene sega ... last none)
+ ! segb should have std 5' (gene segb ... first none)
+ ! USE AUTOgen ANGL DIHE after this patch,
+ ! but before water-generation
+BOND 1O3' 2P
+IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401
+IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802
+IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801
+IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001
+IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996
+
+end
+