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Unverified Commit 06767dde authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Added AMOEBA 2018 force field (#3299) 

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests
parent 610e92fa
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devtools/forcefield-scripts/processTinkerForceField.py
View file @ 06767dde
......@@ -35,16 +35,19 @@ import os.path
# biotype 2006 CA "Calcium Ion" 256
# biotype 2007 CL "Chloride Ion" 258
ions = { 'Li+' : ['LI', 249],
'Na+' : ['NA', 250],
'K+' : ['K', 251],
'Rb+' : ['RB', 252],
'Cs+' : ['CS', 253],
'Be+' : ['BE', 254],
'Mg+' : ['MG', 255],
'Ca+' : ['CA', 256],
'Zn+' : ['ZN', 257],
'Cl-' : ['Cl', 258]
ions = { 'Li+' : ['LI', 351],
'Na+' : ['NA', 352],
'K+' : ['K', 353],
'Rb+' : ['RB', 354],
'Cs+' : ['CS', 355],
'Be2' : ['BE', 356],
'Mg2' : ['MG', 357],
'Ca2' : ['CA', 358],
'Zn2' : ['ZN', 359],
'F-' : ['F', 360],
'Cl-' : ['Cl', 361],
'Br-' : ['Br', 362],
'I-' : ['I', 363]
}
atomTypes = {}
......@@ -149,9 +152,9 @@ def buildProteinResidue( residueDict, atoms, bondInfo, abbr, loc, tinkerLookupNa
residueDict[abbr]['atoms'][bondedAtom]['bonds'][atom] = 1
residueDict[abbr]['atoms'][atom]['bonds'][bondedAtom] = 1
else:
print "Error: bonded atom=%s not in residue=%s" % ( atom, abbr )
print("Error: bonded atom=%s not in residue=%s" % ( atom, abbr ))
else:
print "Error: bonded atom=%s nt in residue=%s" % ( atom, abbr )
print("Error: bonded atom=%s nt in residue=%s" % ( atom, abbr ))
return
......@@ -204,7 +207,7 @@ def copyProteinResidue( residue ):
def buildResidueDict( residueXmlFileName ):
residueTree = etree.parse(residueXmlFileName)
print "Read %s" % (residueXmlFileName)
print("Read %s" % (residueXmlFileName))
root = residueTree.getroot()
residueDict = dict()
......@@ -262,7 +265,7 @@ def buildResidueDict( residueXmlFileName ):
residueDict[cResidueName]['tinkerLookupName'] = 'C-Terminal ' + 'HIS ' + sub
else:
residueDict[cResidueName]['tinkerLookupName'] = 'C-Terminal ' + abbr + ' ' + sub
print "tinkerLookupName %s %s" % ( abbr, residueDict[cResidueName]['tinkerLookupName'])
print("tinkerLookupName %s %s" % ( abbr, residueDict[cResidueName]['tinkerLookupName']))
else:
residueDict[cResidueName]['tinkerLookupName'] = 'C-Terminal ' + abbr
residueDict[cResidueName]['atoms']['OXT'] = copyAtom( residueDict[abbr]['atoms']['O'] )
......@@ -296,10 +299,10 @@ def buildResidueDict( residueXmlFileName ):
buildProteinResidue( residueDict, atoms, bondInfo, abbr, loc, tinkerName, 1, residueName, type )
print "Start Lookup XML FFFFinal\n\n"
print("Start Lookup XML FFFFinal\n\n")
printXml = 1
if( printXml ):
print "<Residues>"
print("<Residues>")
for resName in sorted( residueDict.keys() ):
if( 'include' in residueDict[resName] and residueDict[resName]['include'] ):
type = residueDict[resName]['type']
......@@ -307,13 +310,13 @@ def buildResidueDict( residueXmlFileName ):
tinkerLookupName = residueDict[resName]['tinkerLookupName']
fullName = residueDict[resName]['residueName']
outputString = """ <Residue abbreviation="%s" loc="%s" type="%s" tinkerLookupName="%s" fullName="%s">""" % (resName, loc, type, tinkerLookupName, fullName )
print "%s" % outputString
print("%s" % outputString)
atomsInfo = residueDict[resName]['atoms']
for atomName in sorted( atomsInfo.keys() ):
tinkerLookupName = atomsInfo[atomName]['tinkerLookupName']
outputString = """ <Atom name="%s" tinkerLookupName="%s" />""" % (atomName, tinkerLookupName)
print "%s" % outputString
print("%s" % outputString)
includedBonds = dict()
for atomName in sorted( atomsInfo.keys() ):
......@@ -327,9 +330,9 @@ def buildResidueDict( residueXmlFileName ):
includedBonds[bondedAtom] = dict()
includedBonds[atomName][bondedAtom] = 1
includedBonds[bondedAtom][atomName] = 1
print "%s" % outputString
print "</Residue>"
print "</Residues>"
print("%s" % outputString)
print("</Residue>")
print("</Residues>")
return residueDict
......@@ -363,13 +366,13 @@ def setBioTypes( bioTypes, residueDict ):
if lookupName in bioTypes:
res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else:
print "For %s lookupName=%s not in biotype" % (atom,lookupName)
print("For %s lookupName=%s not in biotype" % (atom,lookupName))
if( 'parent' in res ):
lookupName = res['atoms'][atom]['tinkerLookupName'] + '_' + res['parent']['tinkerLookupName']
if( lookupName in bioTypes ):
res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else:
print "Missing lookupName=%s from biotype" % (lookupName)
print("Missing lookupName=%s from biotype" % (lookupName))
return 0
#=============================================================================================
......@@ -460,12 +463,16 @@ forces = {}
recognizedForces = {}
recognizedForces['bond'] = 1
recognizedForces['angle'] = 1
recognizedForces['anglep'] = 1
recognizedForces['strbnd'] = 1
recognizedForces['ureybrad'] = 1
recognizedForces['opbend'] = 1
recognizedForces['torsion'] = 1
recognizedForces['pitors'] = 1
recognizedForces['strtors'] = 1
recognizedForces['angtors'] = 1
recognizedForces['vdw'] = 1
recognizedForces['vdwpr'] = 1
recognizedForces['polarize'] = 1
recognizedForces['tortors'] = addTorTor
recognizedForces['multipole'] = addMultipole
......@@ -573,7 +580,7 @@ while lineIndex < len( allLines ):
scalars[fields[0]] = fields[1]
lineIndex += 1
else:
print "Field %s not recognized: line=<%s>" % ( fields[0], allLines[lineIndex] )
print("Field %s not recognized: line=<%s>" % ( fields[0], allLines[lineIndex] ))
lineIndex += 1
#=============================================================================================
......@@ -589,12 +596,12 @@ setBioTypes( bioTypes, residueDict )
tinkerXmlFileName = scalars['forcefield']
tinkerXmlFileName += '.xml'
tinkerXmlFile = open( tinkerXmlFileName, 'w' )
print "Opened %s." % (tinkerXmlFileName)
print("Opened %s." % (tinkerXmlFileName))
gkXmlFileName = scalars['forcefield']
gkXmlFileName += '_gk.xml'
gkXmlFile = open( gkXmlFileName, 'w' )
print "Opened %s." % (gkXmlFileName)
print("Opened %s." % (gkXmlFileName))
today = datetime.date.today().isoformat()
sourceFile = os.path.basename(sys.argv[1])
......@@ -680,7 +687,7 @@ for resname, res in sorted(residueDict.items()):
type = res['atoms'][atom]['type']
typeI = int( type )
if( typeI < 0 ):
print "Error: type=%s for atom=%s of residue=%s" % (type, atom, resname)
print("Error: type=%s for atom=%s of residue=%s" % (type, atom, resname))
tag = " <Atom name=\"%s\" type=\"%s\" />" % (atom, type)
atomIndex[atom] = atomCount
atomCount += 1
......@@ -755,7 +762,7 @@ tinkerXmlFile.write(' </Residue>\n')
# ions
for ion,ionInfo in ions.iteritems():
for ion,ionInfo in ions.items():
outputString = """ <Residue name="%s">\n""" % (ionInfo[0])
outputString += """ <Atom name="%s" type="%s"/>\n""" % (ionInfo[0], str(ionInfo[1]))
outputString += """ </Residue>\n"""
......@@ -792,20 +799,20 @@ if( isAmoeba ):
sextic = float(scalars['angle-sextic'])
outputString = """ <AmoebaAngleForce angle-cubic="%s" angle-quartic="%s" angle-pentic="%s" angle-sextic="%s">""" %( str(cubic), str(quartic), str(pentic), str(sextic) )
tinkerXmlFile.write( "%s\n" % (outputString ) )
angles = forces['angle']
radian = 57.2957795130
radian2 = 4.184/(radian*radian)
for angle in angles:
k = float(angle[3])*radian2
outputString = """ <Angle class1="%s" class2="%s" class3="%s" k="%s" angle1="%s" """ % (angle[0], angle[1], angle[2], str(k), angle[4] )
if( len(angle) > 5 ):
outputString += """ angle2="%s" """ % (angle[5])
if( len(angle) > 6 ):
outputString += """ angle3="%s" """ % (angle[6])
outputString += " /> "
tinkerXmlFile.write( "%s\n" % (outputString ) )
for set in ['angle', 'anglep']:
for angle in forces[set]:
k = float(angle[3])*radian2
outputString = ' <Angle class1="%s" class2="%s" class3="%s" k="%s" angle1="%s"' % (angle[0], angle[1], angle[2], str(k), angle[4] )
if( len(angle) > 5 ):
outputString += ' angle2="%s"' % (angle[5])
if( len(angle) > 6 ):
outputString += ' angle3="%s"' % (angle[6])
outputString += ' inPlane="%s"/>' % (set == 'anglep')
tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaAngleForce>\n" )
#=============================================================================================
......@@ -823,9 +830,12 @@ if( isAmoeba ):
opbends = forces['opbend']
radian2 = 4.184/(radian*radian)
for opbend in opbends:
k = float(opbend[4])*radian2
outputString = """ <Angle class1="%s" class2="%s" class3="%s" class4="%s" k="%s"/>""" % (opbend[0], opbend[1], opbend[2], opbend[3], str(k))
tinkerXmlFile.write( "%s\n" % (outputString ) )
k = float(opbend[4])*radian2
for i in range(4):
if opbend[i] == '0':
opbend[i] = ''
outputString = """ <Angle class1="%s" class2="%s" class3="%s" class4="%s" k="%s"/>""" % (opbend[0], opbend[1], opbend[2], opbend[3], str(k))
tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaOutOfPlaneBendForce>\n" )
#=============================================================================================
......@@ -869,6 +879,26 @@ if( isAmoeba ):
tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaPiTorsionForce>\n" )
#=============================================================================================
# Stretch torsion
tinkerXmlFile.write(' <AmoebaStretchTorsionForce>\n')
for torsion in forces['strtors']:
v = [float(x)*10*4.184 for x in torsion[4:]]
tinkerXmlFile.write(f' <Torsion class1="{torsion[0]}" class2="{torsion[1]}" class3="{torsion[2]}" class4="{torsion[3]}" v11="{v[0]}" v12="{v[1]}" v13="{v[2]}" v21="{v[3]}" v22="{v[4]}" v23="{v[5]}" v31="{v[6]}" v32="{v[7]}" v33="{v[8]}"/>\n')
tinkerXmlFile.write(' </AmoebaStretchTorsionForce>\n')
#=============================================================================================
# Angle torsion
tinkerXmlFile.write(' <AmoebaAngleTorsionForce>\n')
for torsion in forces['angtors']:
v = [float(x)*4.184 for x in torsion[4:]]
tinkerXmlFile.write(f' <Torsion class1="{torsion[0]}" class2="{torsion[1]}" class3="{torsion[2]}" class4="{torsion[3]}" v11="{v[0]}" v12="{v[1]}" v13="{v[2]}" v21="{v[3]}" v22="{v[4]}" v23="{v[5]}"/>\n')
tinkerXmlFile.write(' </AmoebaAngleTorsionForce>\n')
#=============================================================================================
# AmoebaStretchBendForce
......@@ -906,7 +936,7 @@ if( isAmoeba ):
outputString = """ <TorsionTorsionGrid grid="%s" nx="%s" ny="%s" >""" % (str(index), torInfo[5], torInfo[6] )
tinkerXmlFile.write( "%s\n" % (outputString ) )
for (gridIndex, gridEntry) in enumerate(grid):
print "Gxx %d %s" % ( gridIndex, str(gridEntry) )
print("Gxx %d %s" % ( gridIndex, str(gridEntry) ))
if( len( gridEntry ) > 5 ):
f = float( gridEntry[2] )*4.184
fx = float( gridEntry[3] )*4.184
......@@ -930,15 +960,19 @@ if( isAmoeba ):
outputString = """ <AmoebaVdwForce type="%s" radiusrule="%s" radiustype="%s" radiussize="%s" epsilonrule="%s" vdw-13-scale="%s" vdw-14-scale="%s" vdw-15-scale="%s" >""" % (
scalars['vdwtype'], scalars['radiusrule'], scalars['radiustype'], scalars['radiussize'], scalars['epsilonrule'], scalars['vdw-13-scale'], scalars['vdw-14-scale'], scalars['vdw-15-scale'] )
tinkerXmlFile.write( "%s\n" % (outputString ) )
vdws = forces['vdw']
for vdw in vdws:
for vdw in forces['vdw']:
sigma = float(vdw[1])*0.1
epsilon = float(vdw[2])*4.184
if( len(vdw) > 3 ):
reduction = vdw[3]
else:
reduction = 1.0
outputString = """ <Vdw class="%s" sigma="%s" epsilon="%s" reduction="%s" /> """ % (vdw[0], str(sigma), str(epsilon), str(reduction) )
outputString = """ <Vdw class="%s" sigma="%s" epsilon="%s" reduction="%s"/>""" % (vdw[0], str(sigma), str(epsilon), str(reduction))
tinkerXmlFile.write( "%s\n" % (outputString ) )
for pair in forces['vdwpr']:
sigma = float(pair[2])*0.1
epsilon = float(pair[3])*4.184
outputString = """ <Pair class1="%s" class2="%s" sigma="%s" epsilon="%s"/>""" % (pair[0], pair[1], str(sigma), str(epsilon))
tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaVdwForce>\n" )
......@@ -1013,11 +1047,11 @@ if( isAmoeba ):
outputString += "/>"
tinkerXmlFile.write( "%s\n" % (outputString ) )
print m[polarize[0]]
print(m[polarize[0]])
for t in sorted(m):
for k in m[t]:
if t not in m[k]:
print t, k
print(t, k)
tinkerXmlFile.write( " </AmoebaMultipoleForce>\n" )
......@@ -1037,10 +1071,10 @@ if( isAmoeba ):
# radii are set in forcefield.py
for type in sorted( atomTypes ):
print "atom type=%s %s" % ( str(type), str(atomTypes[type]) )
print("atom type=%s %s" % ( str(type), str(atomTypes[type]) ))
for type in sorted( bioTypes ):
print "bio type=%s %s" % ( str(type), str(bioTypes[type]) )
print("bio type=%s %s" % ( str(type), str(bioTypes[type]) ))
multipoleArray = forces['multipole']
for multipoleInfo in multipoleArray:
......@@ -1067,9 +1101,9 @@ if( isAmoeba ):
elif( element == 'Fe' ):
shct = 0.88
else:
print "Warning no overlap scale factor for type=%d element=%s" % (type, element)
print("Warning no overlap scale factor for type=%d element=%s" % (type, element))
else:
print "Warning no overlap scale factor for type=%d " % (type)
print("Warning no overlap scale factor for type=%d " % (type))
outputString = """ <GeneralizedKirkwood type="%s" charge="%s" shct="%s" /> """ % ( axisInfo[0], multipoles[0], str(shct) )
gkXmlFile.write( "%s\n" % (outputString ) )
......
docs-source/usersguide/application/02_running_sims.rst
View file @ 06767dde
......@@ -649,25 +649,28 @@ dielectric constant, and :math:`T` is the temperature in Kelvin.
AMOEBA
------
The AMOEBA polarizable force field provides parameters for proteins, water, and ions.
The AMOEBA polarizable force field provides parameters for proteins, nucleic acids, water, and ions.
.. tabularcolumns:: |l|L|
============================= ================================================================================
File Parameters
============================= ================================================================================
:file:`amoeba2013.xml` AMOEBA 2013\ :cite:`Shi2013`
:file:`amoeba2013_gk.xml` Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2013 force field
:file:`amoeba2018.xml` AMOEBA 2018\ :cite:`Shi2013`
:file:`amoeba2018_gk.xml` Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2018 force field
:file:`amoeba2013.xml` AMOEBA 2013. This force field is deprecated. It is
recommended to use AMOEBA 2018 instead.
:file:`amoeba2013_gk.xml` Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
:file:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead.
recommended to use AMOEBA 2018 instead.
:file:`amoeba2009_gk.xml` Generalized Kirkwood solvation model for use with AMOEBA 2009 force field
============================= ================================================================================
For explicit solvent simulations, just include the single file :file:`amoeba2013.xml`.
For explicit solvent simulations, just include the single file :file:`amoeba2018.xml`.
AMOEBA also supports implicit solvent using a Generalized Kirkwood model. To enable
it, also include :file:`amoeba2013_gk.xml`.
it, also include :file:`amoeba2018_gk.xml`.
The older AMOEBA 2009 force field is provided only for backward compatibility, and is not
The older AMOEBA 2009 and 2013 force fields are provided only for backward compatibility, and are not
recommended for most simulations.
CHARMM Polarizable Force Field
......
wrappers/python/openmm/app/data/amoeba2018.xml 0 → 100644
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wrappers/python/openmm/app/data/amoeba2018_gk.xml 0 → 100644
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wrappers/python/openmm/app/forcefield.py
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wrappers/python/tests/TestForceField.py
View file @ 06767dde
......@@ -1282,7 +1282,7 @@ class AmoebaTestForceField(unittest.TestCase):
forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
system = forcefield.createSystem(pdb.topology, polarization='direct')
integrator = VerletIntegrator(0.001)
context = Context(system, integrator)
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
context.setPositions(pdb.positions)
state1 = context.getState(getForces=True)
with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
......@@ -1291,6 +1291,55 @@ class AmoebaTestForceField(unittest.TestCase):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
def computeAmoeba18Energies(self, filename):
pdb = PDBFile(filename)
forcefield = ForceField('amoeba2018.xml')
system = forcefield.createSystem(pdb.topology, polarization='mutual', mutualInducedTargetEpsilon=1e-5)
for i, f in enumerate(system.getForces()):
f.setForceGroup(i)
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
context.setPositions(pdb.positions)
energies = {}
for i, f in enumerate(system.getForces()):
state = context.getState(getEnergy=True, groups={i})
energies[f.getName()] = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
return energies
def test_Amoeba18BPTI(self):
"""Test that AMOEBA18 computes energies correctly for BPTI."""
energies = self.computeAmoeba18Energies('systems/bpti.pdb')
# Compare to values computed with Tinker.
self.assertAlmostEqual(290.2445, energies['AmoebaBond'], 4)
self.assertAlmostEqual(496.4300, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4)
self.assertAlmostEqual(51.2913, energies['AmoebaOutOfPlaneBend'], 4)
self.assertAlmostEqual(5.7695, energies['AmoebaStretchBend'], 4)
self.assertAlmostEqual(75.6890, energies['PeriodicTorsionForce'], 4)
self.assertAlmostEqual(19.3364, energies['AmoebaPiTorsion'], 4)
self.assertAlmostEqual(-32.6689, energies['AmoebaTorsionTorsionForce'], 4)
self.assertAlmostEqual(383.8705, energies['AmoebaVdwForce'], 4)
self.assertAlmostEqual(-1323.5640-225.3660, energies['AmoebaMultipoleForce'], 2)
self.assertAlmostEqual(-258.9676, sum(list(energies.values())), 2)
def test_Amoeba18DNA(self):
"""Test that AMOEBA18 computes energies correctly for DNA."""
energies = self.computeAmoeba18Energies('systems/dna.pdb')
# Compare to values computed with Tinker.
self.assertAlmostEqual(688.7794, energies['AmoebaBond'], 4)
self.assertAlmostEqual(430.5887, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4)
self.assertAlmostEqual(10.5715, energies['AmoebaOutOfPlaneBend'], 4)
self.assertAlmostEqual(0.7773, energies['AmoebaStretchBend'], 4)
self.assertAlmostEqual(77.0482, energies['PeriodicTorsionForce'], 4)
self.assertAlmostEqual(56.5654, energies['AmoebaPiTorsion'], 4)
self.assertAlmostEqual(-0.5457, energies['AmoebaStretchTorsion'], 4)
self.assertAlmostEqual(-1.6044, energies['AmoebaAngleTorsion'], 4)
self.assertAlmostEqual(106.4062, energies['AmoebaVdwForce'], 4)
self.assertAlmostEqual(90.5715-73.6051, energies['AmoebaMultipoleForce'], 4)
self.assertAlmostEqual(1385.5529, sum(list(energies.values())), 4)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/dna.pdb 0 → 100644
View file @ 06767dde
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