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Commit b5da7380 authored by peastman's avatar peastman
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Merge pull request #179 from swails/master 

Implement GBn2 (same as igb==8 in Amber), a significantly improved GB model
parents 9c666133 844b38d9
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Showing with 177 additions and 62 deletions
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ b5da7380
...@@ -61,6 +61,11 @@ class GBn(object): ...@@ -61,6 +61,11 @@ class GBn(object):
return 'GBn' return 'GBn'
GBn = GBn() GBn = GBn()
class GBn2(object):
def __repr__(self):
return 'GBn2'
GBn2 = GBn2()
class AmberPrmtopFile(object): class AmberPrmtopFile(object):
"""AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.""" """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
...@@ -69,6 +74,7 @@ class AmberPrmtopFile(object): ...@@ -69,6 +74,7 @@ class AmberPrmtopFile(object):
top = Topology() top = Topology()
## The Topology read from the prmtop file ## The Topology read from the prmtop file
self.topology = top self.topology = top
self.elements = []
# Load the prmtop file # Load the prmtop file
...@@ -96,7 +102,14 @@ class AmberPrmtopFile(object): ...@@ -96,7 +102,14 @@ class AmberPrmtopFile(object):
if atomName in atomReplacements: if atomName in atomReplacements:
atomName = atomReplacements[atomName] atomName = atomReplacements[atomName]
# Try to guess the element. # Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper() upper = atomName.upper()
if upper.startswith('CL'): if upper.startswith('CL'):
...@@ -110,7 +123,9 @@ class AmberPrmtopFile(object): ...@@ -110,7 +123,9 @@ class AmberPrmtopFile(object):
element = elem.get_by_symbol(atomName[0]) element = elem.get_by_symbol(atomName[0])
except KeyError: except KeyError:
element = None element = None
top.addAtom(atomName, element, r) top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology # Add bonds to the topology
...@@ -137,7 +152,7 @@ class AmberPrmtopFile(object): ...@@ -137,7 +152,7 @@ class AmberPrmtopFile(object):
- constraints (object=None) Specifies which bonds angles should be implemented with constraints. - constraints (object=None) Specifies which bonds angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles. Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn. - implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model. - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model. - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
...@@ -167,19 +182,22 @@ class AmberPrmtopFile(object): ...@@ -167,19 +182,22 @@ class AmberPrmtopFile(object):
raise ValueError('Illegal value for constraints') raise ValueError('Illegal value for constraints')
if implicitSolvent is None: if implicitSolvent is None:
implicitString = None implicitString = None
elif implicitSolvent == HCT: elif implicitSolvent is HCT:
implicitString = 'HCT' implicitString = 'HCT'
elif implicitSolvent == OBC1: elif implicitSolvent is OBC1:
implicitString = 'OBC1' implicitString = 'OBC1'
elif implicitSolvent == OBC2: elif implicitSolvent is OBC2:
implicitString = 'OBC2' implicitString = 'OBC2'
elif implicitSolvent == GBn: elif implicitSolvent is GBn:
implicitString = 'GBn' implicitString = 'GBn'
elif implicitSolvent is GBn2:
implicitString = 'GBn2'
else: else:
raise ValueError('Illegal value for implicit solvent model') raise ValueError('Illegal value for implicit solvent model')
sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff, sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString, nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater) soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater,
elements=self.elements)
if hydrogenMass is not None: if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds(): for atom1, atom2 in self.topology.bonds():
if atom1.element == elem.hydrogen: if atom1.element == elem.hydrogen:
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ b5da7380
...@@ -52,6 +52,7 @@ except: ...@@ -52,6 +52,7 @@ except:
import simtk.unit as units import simtk.unit as units
import simtk.openmm import simtk.openmm
from simtk.openmm.app import element as elem
import customgbforces as customgb import customgbforces as customgb
#============================================================================================= #=============================================================================================
...@@ -472,34 +473,74 @@ class PrmtopLoader(object): ...@@ -472,34 +473,74 @@ class PrmtopLoader(object):
self._excludedAtoms.append(atomList) self._excludedAtoms.append(atomList)
return self._excludedAtoms return self._excludedAtoms
def getGBParms(self, symbls=None): def getGBParms(self, gbmodel, elements):
"""Return list giving GB params, Radius and screening factor""" """Return list giving GB params, Radius and screening factor"""
try: gb_List=[]
return self._gb_List radii=[float(r) for r in self._raw_data["RADII"]]
except AttributeError: screen=[float(s) for s in self._raw_data["SCREEN"]]
pass if gbmodel == 'GBn2':
self._gb_List=[] alpha = [0 for i in self._raw_data['RADII']]
radii=self._raw_data["RADII"] beta = [0 for i in self._raw_data['RADII']]
screen=self._raw_data["SCREEN"] gamma = [0 for i in self._raw_data['RADII']]
# Update screening parameters for GBn if specified # Update screening parameters for GBn if specified
if symbls: if gbmodel == 'GBn':
for (i, symbl) in enumerate(symbls): if elements is None:
if symbl[0] in ('c', 'C'): raise Exception('GBn model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 0.48435382330 screen[i] = 0.48435382330
elif symbl[0] in ('h', 'H'): elif element is elem.hydrogen:
screen[i] = 1.09085413633 screen[i] = 1.09085413633
elif symbl[0] in ('n', 'N'): elif element is elem.nitrogen:
screen[i] = 0.700147318409 screen[i] = 0.700147318409
elif symbl[0] in ('o', 'O'): elif element is elem.oxygen:
screen[i] = 1.06557401132 screen[i] = 1.06557401132
elif symbl[0] in ('s', 'S'): elif element is elem.sulfur:
screen[i] = 0.602256336067 screen[i] = 0.602256336067
else: else:
screen[i] = 0.5 screen[i] = 0.5
if gbmodel == 'GBn2':
if elements is None:
raise Exception('GBn2 model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif element is elem.hydrogen:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif element is elem.nitrogen:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif element is elem.oxygen:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif element is elem.sulfur:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else: # not optimized
screen[i] = 0.5
alpha[i] = 1.0
beta[i] = 0.8
gamma[i] = 4.85
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer) lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
for iAtom in range(len(radii)): if gbmodel == 'GBn2':
self._gb_List.append((float(radii[iAtom])*lengthConversionFactor, float(screen[iAtom]))) for rad, scr, alp, bet, gam in zip(radii, screen, alpha, beta, gamma):
return self._gb_List gb_List.append((rad*lengthConversionFactor, scr, alp, bet, gam))
else:
for rad, scr in zip(radii, screen):
gb_List.append((rad*lengthConversionFactor, scr))
return gb_List
def getBoxBetaAndDimensions(self): def getBoxBetaAndDimensions(self):
"""Return periodic boundary box beta angle and dimensions""" """Return periodic boundary box beta angle and dimensions"""
...@@ -516,11 +557,17 @@ class PrmtopLoader(object): ...@@ -516,11 +557,17 @@ class PrmtopLoader(object):
def has_scee_scnb(self): def has_scee_scnb(self):
return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data) return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data)
@property
def has_atomic_number(self):
return 'ATOMIC_NUMBER' in self._raw_data
#============================================================================================= #=============================================================================================
# AMBER System builder (based on, but not identical to, systemManager from 'zander') # AMBER System builder (based on, but not identical to, systemManager from 'zander')
#============================================================================================= #=============================================================================================
def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True): def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5,
nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True, elements=None):
""" """
Create an OpenMM System from an Amber prmtop file. Create an OpenMM System from an Amber prmtop file.
...@@ -813,15 +860,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -813,15 +860,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if gbmodel is not None: if gbmodel is not None:
if verbose: print "Adding GB parameters..." if verbose: print "Adding GB parameters..."
charges = prmtop.getCharges() charges = prmtop.getCharges()
symbls = None
cutoff = None cutoff = None
if nonbondedMethod != 'NoCutoff': if nonbondedMethod != 'NoCutoff':
cutoff = nonbondedCutoff cutoff = nonbondedCutoff
if units.is_quantity(cutoff): if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers) cutoff = cutoff.value_in_unit(units.nanometers)
if gbmodel == 'GBn': gb_parms = prmtop.getGBParms(gbmodel, elements)
symbls = prmtop.getAtomTypes()
gb_parms = prmtop.getGBParms(symbls)
if gbmodel == 'HCT': if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff) gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'OBC1': elif gbmodel == 'OBC1':
...@@ -832,11 +876,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -832,11 +876,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
gb.setSolventDielectric(solventDielectric) gb.setSolventDielectric(solventDielectric)
elif gbmodel == 'GBn': elif gbmodel == 'GBn':
gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff) gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'GBn2':
gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff)
else: else:
raise Exception("Illegal value specified for implicit solvent model") raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()): for iAtom in range(prmtop.getNumAtoms()):
if gbmodel == 'OBC2': if gbmodel == 'OBC2':
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]) gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
elif gbmodel == 'GBn2':
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
else: else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]]) gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
system.addForce(gb) system.addForce(gb)
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ b5da7380
...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org. ...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012 University of Virginia and the Authors. Portions copyright (c) 2012 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts Authors: Christoph Klein, Michael R. Shirts
Contributors: Contributors: Jason M. Swails
Permission is hereby granted, free of charge, to any person obtaining a Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"), copy of this software and associated documentation files (the "Software"),
...@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE ...@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE. USE OR OTHER DEALINGS IN THE SOFTWARE.
""" """
from __future__ import division
from simtk.openmm import CustomGBForce from simtk.openmm import CustomGBForce
import sys, pdb, pickle
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444, d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196, 2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
...@@ -212,11 +213,11 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -212,11 +213,11 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -237,11 +238,11 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No ...@@ -237,11 +238,11 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -262,11 +263,11 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No ...@@ -262,11 +263,11 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -296,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -296,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825) custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68) custom.addGlobalParameter("neckCut", 0.68)
...@@ -323,3 +324,50 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -323,3 +324,50 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff) _createEnergyTerms(custom, SA, cutoff)
return custom return custom
"""
Amber Equivalents: igb = 8
"""
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.0195141)
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom
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