customgbforces.py

"""
A recreation of the various GB variants implemented via CustomGBForce

This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2012 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts
Contributors: Jason M. Swails

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""

from __future__ import division

from simtk.openmm import CustomGBForce

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,
    3.18854,3.24498,3.30132,3.35752,3.4136,
    2.31191,2.37017,2.4283,2.48632,2.5442,2.60197,2.65961,2.71711,
    2.77449,2.83175,2.88887,2.94586,3.00273,3.05948,3.1161,3.1726,
    3.22897,3.28522,3.34136,3.39738,3.45072,
    2.35759,2.41549,2.47329,2.53097,2.58854,2.646,2.70333,2.76056,
    2.81766,2.87465,2.93152,2.98827,3.0449,3.10142,3.15782,3.21411,
    3.27028,3.32634,3.3823,3.43813,3.49387,
    2.4038,2.46138,2.51885,2.57623,2.63351,2.69067,2.74773,2.80469,
    2.86152,2.91826,2.97489,3.0314,3.08781,3.1441,3.20031,3.25638,
    3.31237,3.36825,3.42402,3.4797,3.53527,
    2.45045,2.50773,2.56492,2.62201,2.679,2.7359,2.7927,2.8494,2.90599,
    2.9625,3.0189,3.07518,3.13138,3.18748,3.24347,3.29937,3.35515,
    3.41085,3.46646,3.52196,3.57738,
    2.4975,2.5545,2.61143,2.66825,2.72499,2.78163,2.83818,2.89464,
    2.95101,3.00729,3.06346,3.11954,3.17554,3.23143,3.28723,3.34294,
    3.39856,3.45409,3.50952,3.56488,3.62014,
    2.54489,2.60164,2.6583,2.71488,2.77134,2.8278,2.88412,2.94034,
    2.9965,3.05256,3.10853,3.16442,3.22021,3.27592,3.33154,3.38707,
    3.44253,3.49789,3.55316,3.60836,3.66348,
    2.59259,2.6491,2.70553,2.76188,2.81815,2.87434,2.93044,2.98646,
    3.04241,3.09827,3.15404,3.20974,3.26536,3.32089,3.37633,3.4317,
    3.48699,3.54219,3.59731,3.65237,3.70734,
    2.64054,2.69684,2.75305,2.80918,2.86523,2.92122,2.97712,3.03295,
    3.0887,3.14437,3.19996,3.25548,3.31091,3.36627,3.42156,3.47677,
    3.5319,3.58695,3.64193,3.69684,3.75167,
    2.68873,2.74482,2.80083,2.85676,2.91262,2.96841,3.02412,3.07976,
    3.13533,3.19082,3.24623,3.30157,3.35685,3.41205,3.46718,3.52223,
    3.57721,3.63213,3.68696,3.74174,3.79644,
    2.73713,2.79302,2.84884,2.90459,2.96027,3.01587,3.0714,3.12686,
    3.18225,3.23757,3.29282,3.34801,3.40313,3.45815,3.51315,3.56805,
    3.6229,3.67767,3.73237,3.78701,3.84159,
    2.78572,2.84143,2.89707,2.95264,3.00813,3.06356,3.11892,3.17422,
    3.22946,3.28462,3.33971,3.39474,3.44971,3.5046,3.55944,3.61421,
    3.66891,3.72356,3.77814,3.83264,3.8871,
    2.83446,2.89,2.94547,3.00088,3.05621,3.11147,3.16669,3.22183,
    3.27689,3.33191,3.38685,3.44174,3.49656,3.55132,3.60602,3.66066,
    3.71523,3.76975,3.82421,3.8786,3.93293,
    2.88335,2.93873,2.99404,3.04929,3.10447,3.15959,3.21464,3.26963,
    3.32456,3.37943,3.43424,3.48898,3.54366,3.5983,3.65287,3.70737,
    3.76183,3.81622,3.87056,3.92484,3.97905,
    2.93234,2.9876,3.04277,3.09786,3.15291,3.20787,3.26278,3.31764,
    3.37242,3.42716,3.48184,3.53662,3.591,3.64551,3.69995,3.75435,
    3.80867,3.86295,3.91718,3.97134,4.02545,
    2.98151,3.0366,3.09163,3.14659,3.20149,3.25632,3.3111,3.36581,
    3.42047,3.47507,3.52963,3.58411,3.63855,3.69293,3.74725,3.80153,
    3.85575,3.90991,3.96403,4.01809,4.07211,
    3.03074,3.08571,3.14061,3.19543,3.25021,3.30491,3.35956,3.41415,
    3.46869,3.52317,3.57759,3.63196,3.68628,3.74054,3.79476,3.84893,
    3.90303,3.95709,4.01111,4.06506,4.11897,
    3.08008,3.13492,3.1897,3.2444,3.29905,3.35363,3.40815,3.46263,
    3.51704,3.57141,3.62572,3.67998,3.73418,3.78834,3.84244,3.8965,
    3.95051,4.00447,4.05837,4.11224,4.16605,
    3.12949,3.18422,3.23888,3.29347,3.348,3.40247,3.45688,3.51124,
    3.56554,3.6198,3.674,3.72815,3.78225,3.83629,3.8903,3.94425,
    3.99816,4.05203,4.10583,4.15961,4.21333,
    3.17899,3.23361,3.28815,3.34264,3.39706,3.45142,3.50571,3.55997,
    3.61416,3.66831,3.72241,3.77645,3.83046,3.8844,3.93831,3.99216,
    4.04598,4.09974,4.15347,4.20715,4.26078,
    3.22855,3.28307,3.33751,3.39188,3.4462,3.50046,3.55466,3.6088,
    3.6629,3.71694,3.77095,3.82489,3.8788,3.93265,3.98646,4.04022,
    4.09395,4.14762,4.20126,4.25485,4.3084]



m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
    0.0197547,0.0179109,0.0162844,0.0148442,0.0135647,0.0124243,
    0.0114047,0.0104906,0.00966876,0.008928,0.0082587,0.00765255,
    0.00710237,0.00660196,0.00614589,
    0.0396198,0.0351837,0.0313767,0.0280911,0.0252409,0.0227563,
    0.0205808,0.0186681,0.0169799,0.0154843,0.014155,0.0129696,
    0.0119094,0.0109584,0.0101031,0.00933189,0.0086348,0.00800326,
    0.00742986,0.00690814,0.00643255,
    0.041048,0.0364738,0.0325456,0.0291532,0.0262084,0.0236399,
    0.0213897,0.0194102,0.0176622,0.0161129,0.0147351,0.0135059,
    0.0124061,0.0114192,0.0105312,0.00973027,0.00900602,0.00834965,
    0.0077535,0.00721091,0.00671609,
    0.0424365,0.0377295,0.0336846,0.0301893,0.0271533,0.0245038,
    0.0221813,0.0201371,0.018331,0.0167295,0.0153047,0.014033,
    0.0128946,0.0118727,0.0109529,0.0101229,0.00937212,0.00869147,
    0.00807306,0.00751003,0.00699641,
    0.0437861,0.0389516,0.0347944,0.0311998,0.0280758,0.0253479,
    0.0229555,0.0208487,0.0189864,0.0173343,0.0158637,0.0145507,
    0.0133748,0.0123188,0.0113679,0.0105096,0.0097329,0.00902853,
    0.00838835,0.00780533,0.0072733,
    0.0450979,0.0401406,0.0358753,0.0321851,0.0289761,0.0261726,
    0.0237125,0.0215451,0.0196282,0.017927,0.0164121,0.0150588,
    0.0138465,0.0127573,0.0117761,0.0108902,0.0100882,0.00936068,
    0.00869923,0.00809665,0.00754661,
    0.0463729,0.0412976,0.0369281,0.0331456,0.0298547,0.026978,
    0.0244525,0.0222264,0.0202567,0.0185078,0.0169498,0.0155575,
    0.0143096,0.0131881,0.0121775,0.0112646,0.010438,0.00968781,
    0.00900559,0.00838388,0.00781622,
    0.0476123,0.0424233,0.0379534,0.034082,0.0307118,0.0277645,
    0.0251757,0.0228927,0.0208718,0.0190767,0.0174768,0.0160466,
    0.0147642,0.0136112,0.0125719,0.0116328,0.0107821,0.0100099,
    0.00930735,0.00866695,0.00808206,
    0.0488171,0.0435186,0.038952,0.0349947,0.0315481,0.0285324,
    0.0258824,0.0235443,0.0214738,0.0196339,0.0179934,0.0165262,
    0.0152103,0.0140267,0.0129595,0.0119947,0.0111206,0.0103268,
    0.00960445,0.00894579,0.00834405,
    0.0499883,0.0445845,0.0399246,0.0358844,0.032364,0.0292822,
    0.0265729,0.0241815,0.0220629,0.0201794,0.0184994,0.0169964,
    0.0156479,0.0144345,0.0133401,0.0123504,0.0114534,0.0106386,
    0.00989687,0.00922037,0.00860216,
    0.0511272,0.0456219,0.040872,0.0367518,0.0331599,0.0300142,
    0.0272475,0.0248045,0.0226392,0.0207135,0.0189952,0.0174574,
    0.0160771,0.0148348,0.0137138,0.0126998,0.0117805,0.0109452,
    0.0101846,0.00949067,0.00885636,
    0.0522348,0.0466315,0.0417948,0.0375973,0.0339365,0.030729,
    0.0279067,0.0254136,0.023203,0.0212363,0.0194809,0.0179092,
    0.016498,0.0152275,0.0140807,0.013043,0.012102,0.0112466,
    0.0104676,0.00975668,0.00910664,
    0.0533123,0.0476145,0.042694,0.0384218,0.0346942,0.0314268,
    0.0285507,0.026009,0.0237547,0.0217482,0.0199566,0.018352,
    0.0169108,0.0156128,0.0144408,0.0133801,0.0124179,0.011543,
    0.010746,0.0100184,0.00935302,
    0.0543606,0.0485716,0.04357,0.0392257,0.0354335,0.0321082,
    0.02918,0.0265913,0.0242943,0.0222492,0.0204225,0.0187859,
    0.0173155,0.0159908,0.0147943,0.0137111,0.0127282,0.0118343,
    0.0110197,0.0102759,0.00959549,
    0.0553807,0.0495037,0.0444239,0.0400097,0.0361551,0.0327736,
    0.0297949,0.0271605,0.0248222,0.0227396,0.0208788,0.0192111,
    0.0177122,0.0163615,0.0151413,0.0140361,0.013033,0.0121206,
    0.0112888,0.0105292,0.00983409,
    0.0563738,0.0504116,0.0452562,0.0407745,0.0368593,0.0334235,
    0.0303958,0.0277171,0.0253387,0.0232197,0.0213257,0.0196277,
    0.0181013,0.0167252,0.0154817,0.0143552,0.0133325,0.0124019,
    0.0115534,0.0107783,0.0100688,
    0.0573406,0.0512963,0.0460676,0.0415206,0.0375468,0.0340583,
    0.030983,0.0282614,0.0258441,0.0236896,0.0217634,0.020036,
    0.0184826,0.017082,0.0158158,0.0146685,0.0136266,0.0126783,
    0.0118135,0.0110232,0.0102998,
    0.0582822,0.0521584,0.0468589,0.0422486,0.038218,0.0346784,
    0.0315571,0.0287938,0.0263386,0.0241497,0.0221922,0.0204362,
    0.0188566,0.0174319,0.0161437,0.0149761,0.0139154,0.0129499,
    0.0120691,0.0112641,0.0105269,
    0.0591994,0.0529987,0.0476307,0.042959,0.0388734,0.0352843,
    0.0321182,0.0293144,0.0268225,0.0246002,0.0226121,0.0208283,
    0.0192232,0.0177751,0.0164654,0.015278,0.0141991,0.0132167,
    0.0123204,0.0115009,0.0107504,
    0.0600932,0.053818,0.0483836,0.0436525,0.0395136,0.0358764,
    0.0326669,0.0298237,0.0272961,0.0250413,0.0230236,0.0212126,
    0.0195826,0.0181118,0.0167811,0.0155744,0.0144778,0.0134789,
    0.0125673,0.0117338,0.0109702,
    0.0609642,0.0546169,0.0491183,0.0443295,0.0401388,0.036455,
    0.0332033,0.030322,0.0277596,0.0254732,0.0234266,0.0215892,
    0.0199351,0.018442,0.0170909,0.0158654,0.0147514,0.0137365,
    0.0128101,0.0119627,0.0111863]
# Rescale to nm
for i in range (len(d0)):
    d0[i]=d0[i]/10
    m0[i]=m0[i]*10


def _createEnergyTerms(force, SA, cutoff, kappa):
    # Add the energy terms to the CustomGBForce.  These are identical for all the GB models.
    
    if kappa > 0:
        force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*q^2/B",
                CustomGBForce.SingleParticle)
    elif kappa < 0:
        # Do kappa check here to avoid repeating code everywhere
        raise ValueError('kappa/ionic strength must be >= 0')
    else:
        force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B",
                CustomGBForce.SingleParticle)
    if SA=='ACE':
        force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
    elif SA is not None:
        raise ValueError('Unknown surface area method: '+SA)
    if cutoff is None:
        if kappa > 0:
            force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2/f;"
                                "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
        else:
            force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
                                "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
    else:
        if kappa > 0:
            force.addEnergyTerm("-138.935485*(1/soluteDielectric-kappa/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
                                "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
        else:
            force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
                                "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)

"""
Amber Equivalent: igb = 1
"""


def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
                 cutoff=None, kappa=0.0):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    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);"
                                  "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-I);"
                                  "or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom

"""
Amber Equivalents: igb = 2
"""
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    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);"
                                  "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(0.8*psi+2.909125*psi^3)/radius);"
                                  "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom

"""
Amber Equivalents: igb = 5
"""
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    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);"
                                  "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(psi-0.8*psi^2+4.85*psi^3)/radius);"
                                  "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom

"""
Amber Equivalents: igb = 7
"""
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):


    """
    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")

    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.009)
    custom.addGlobalParameter("neckScale", 0.361825)
    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(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
                              "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom

"""
Amber Equivalents: igb = 8
"""
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):


    """
    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")

    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    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, kappa)
    return custom