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Commit dce2d427 authored by Peter Eastman's avatar Peter Eastman
Browse files

Added Christoph Klein's implementation of AMBER GB models as custom forces

parent 724e498b
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Showing with 378 additions and 24 deletions
wrappers/python/simtk/openmm/app/__init__.py
View file @ dce2d427
...@@ -34,4 +34,7 @@ HBonds = forcefield.HBonds ...@@ -34,4 +34,7 @@ HBonds = forcefield.HBonds
AllBonds = forcefield.AllBonds AllBonds = forcefield.AllBonds
HAngles = forcefield.HAngles HAngles = forcefield.HAngles
OBC = amberprmtopfile.OBC HCT = amberprmtopfile.HCT
OBC1 = amberprmtopfile.OBC1
OBC2 = amberprmtopfile.OBC2
GBn = amberprmtopfile.GBn
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ dce2d427
...@@ -14,7 +14,10 @@ import simtk.openmm as mm ...@@ -14,7 +14,10 @@ import simtk.openmm as mm
# Enumerated values for implicit solvent model # Enumerated values for implicit solvent model
OBC = object() HCT = object()
OBC1 = object()
OBC2 = object()
GBn = object()
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."""
...@@ -79,7 +82,7 @@ class AmberPrmtopFile(object): ...@@ -79,7 +82,7 @@ class AmberPrmtopFile(object):
top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer) top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer, def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, implicitSolvent=None, removeCMMotion=True): constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, removeCMMotion=True):
"""Construct an OpenMM System representing the topology described by this prmtop file. """Construct an OpenMM System representing the topology described by this prmtop file.
Parameters: Parameters:
...@@ -89,7 +92,9 @@ class AmberPrmtopFile(object): ...@@ -89,7 +92,9 @@ 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 - implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn.
- 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.
- 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
Returns: the newly created System Returns: the newly created System
""" """
...@@ -116,12 +121,19 @@ class AmberPrmtopFile(object): ...@@ -116,12 +121,19 @@ 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 == OBC: elif implicitSolvent == HCT:
implicitString = 'OBC' implicitString = 'HCT'
elif implicitSolvent == OBC1:
implicitString = 'OBC1'
elif implicitSolvent == OBC2:
implicitString = 'OBC2'
elif implicitSolvent == GBn:
implicitString = 'GBn'
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, rigidWater=rigidWater) nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater)
if removeCMMotion: if removeCMMotion:
sys.addForce(mm.CMMotionRemover()) sys.addForce(mm.CMMotionRemover())
return sys return sys
\ No newline at end of file
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ dce2d427
...@@ -32,6 +32,7 @@ except: ...@@ -32,6 +32,7 @@ except:
import simtk.unit as units import simtk.unit as units
import simtk.openmm import simtk.openmm
import customgbforces as customgb
#============================================================================================= #=============================================================================================
# AMBER parmtop loader (from 'zander', by Randall J. Radmer) # AMBER parmtop loader (from 'zander', by Randall J. Radmer)
...@@ -439,21 +440,33 @@ class PrmtopLoader(object): ...@@ -439,21 +440,33 @@ class PrmtopLoader(object):
self._excludedAtoms.append(atomList) self._excludedAtoms.append(atomList)
return self._excludedAtoms return self._excludedAtoms
def getGBSA_OBC(self): def getGBParms(self, symbls=None):
"""Return list giving GB params, Radius and screening factor""" """Return list giving GB params, Radius and screening factor"""
try: try:
return self._gbsa_obcList return self._gb_List
except AttributeError: except AttributeError:
pass pass
self._gbsa_obcList=[] self._gb_List=[]
radii=self._raw_data["RADII"] radii=self._raw_data["RADII"]
screen=self._raw_data["SCREEN"] screen=self._raw_data["SCREEN"]
# Update screening parameters for GBn if specified
if symbls:
for (i, symbl) in enumerate(symbls):
if symbl[0] == ('c' or 'C'):
screen[i] = 0.48435382330
elif symbl[0] == ('h' or 'H'):
screen[i] = 1.09085413633
elif symbl[0] == ('n' or 'N'):
screen[i] = 0.700147318409
elif symbl[0] == ('o' or 'O'):
screen[i] = 1.06557401132
elif symbl[0] == ('s' or 'S'):
screen[i] = 0.602256336067
else:
screen[i] = 0.5
for iAtom in range(len(radii)): for iAtom in range(len(radii)):
self._gbsa_obcList.append( (units.Quantity(float(radii[iAtom]), self._gb_List.append((float(radii[iAtom])*units.angstrom, float(screen[iAtom])))
units.angstrom), return self._gb_List
units.Quantity(float(screen[iAtom]),
units.dimensionless)) )
return self._gbsa_obcList
def getBoxBetaAndDimensions(self): def getBoxBetaAndDimensions(self):
"""Return periodic boundary box beta angle and dimensions""" """Return periodic boundary box beta angle and dimensions"""
...@@ -470,7 +483,7 @@ class PrmtopLoader(object): ...@@ -470,7 +483,7 @@ class PrmtopLoader(object):
# 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, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=1.2, scnb=2.0, 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=1.2, scnb=2.0, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
""" """
Create an OpenMM System from an Amber prmtop file. Create an OpenMM System from an Amber prmtop file.
...@@ -481,6 +494,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -481,6 +494,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
OPTIONAL ARGUMENTS OPTIONAL ARGUMENTS
shake (String) - if 'h-bonds', will SHAKE all bonds to hydrogen and water; if 'all-bonds', will SHAKE all bonds and water (default: None) shake (String) - if 'h-bonds', will SHAKE all bonds to hydrogen and water; if 'all-bonds', will SHAKE all bonds and water (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be used; if 'GBVI', GB/VI will be used (default: None) gbmodel (String) - if 'OBC', OBC GBSA will be used; if 'GBVI', GB/VI will be used (default: None)
soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None) nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None)
scnb (float) - 1-4 Lennard-Jones scaling factor (default: 1.2) scnb (float) - 1-4 Lennard-Jones scaling factor (default: 1.2)
scee (float) - 1-4 electrostatics scaling factor (default: 2.0) scee (float) - 1-4 electrostatics scaling factor (default: 2.0)
...@@ -746,15 +761,31 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -746,15 +761,31 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
system.setVirtualSite(waterEP[res][0], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, weightCross)) system.setVirtualSite(waterEP[res][0], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, weightCross))
system.setVirtualSite(waterEP[res][1], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, -weightCross)) system.setVirtualSite(waterEP[res][1], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, -weightCross))
# Add GBSA-OBC model. # Add GBSA model.
if gbmodel == 'OBC': if gbmodel is not None:
if verbose: print "Adding GB parameters..." if verbose: print "Adding GB parameters..."
gb = mm.GBSAOBCForce()
charges = prmtop.getCharges() charges = prmtop.getCharges()
gbsa_obc = prmtop.getGBSA_OBC() symbls = None
#for charge, radius, scalingFactor in prmtop.getGBSA_OBC(): if gbmodel == 'GBn':
symbls = prmtop.getAtomTypes()
gb_parms = prmtop.getGBParms(symbls)
if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, True)
elif gbmodel == 'OBC1':
gb = customgb.GBSAOBC1Force(solventDielectric, soluteDielectric, True)
elif gbmodel == 'OBC2':
gb = mm.GBSAOBCForce()
gb.setSoluteDielectric(soluteDielectric)
gb.setSolventDielectric(solventDielectric)
elif gbmodel == 'GBn':
gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, True)
else:
raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()): for iAtom in range(prmtop.getNumAtoms()):
gb.addParticle(charges[iAtom], gbsa_obc[iAtom][0], gbsa_obc[iAtom][1]) if gbmodel == 'OBC2':
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
system.addForce(gb) system.addForce(gb)
if nonbondedMethod == 'NoCutoff': if nonbondedMethod == 'NoCutoff':
gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff) gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py 0 → 100644
View file @ dce2d427
"""
A recreation of the various GB variants implemented via 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,
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
"""
Amber Equivalent: igb = 1
"""
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
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)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom
"""
Amber Equivalents: igb = 2
"""
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
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)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom
"""
Amber Equivalents: igb = 5
"""
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
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)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom
"""
Amber Equivalents: igb = 7
"""
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=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.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)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom
\ No newline at end of file
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