Skip to content

GitLab

"platforms/reference/vscode:/vscode.git/clone" did not exist on "88da682c3bce6ec1ee12c8b773b29e1d8207d4bb"
Commit 4d32047c authored by peastman's avatar peastman
Browse files

Merge pull request #1279 from peastman/nucleic 

Support nucleic acids in AMOEBA 2009
parents 42b7ccd3 69d7dc4f
Hide whitespace changes
Inline Side-by-side
Showing with 13920 additions and 9583 deletions
devtools/forcefield-scripts/processTinkerForceField.py
View file @ 4d32047c
...@@ -35,16 +35,16 @@ import os.path ...@@ -35,16 +35,16 @@ import os.path
# biotype 2006 CA "Calcium Ion" 256 # biotype 2006 CA "Calcium Ion" 256
# biotype 2007 CL "Chloride Ion" 258 # biotype 2007 CL "Chloride Ion" 258
ions = { 'Li+' : [ 'LI', 249, 249 ], ions = { 'Li+' : ['LI', 249],
'Na+' : [ 'NA', 250, 2003 ], 'Na+' : ['NA', 250],
'K+' : [ 'K', 251, 2004 ], 'K+' : ['K', 251],
'Rb+' : [ 'RB', 252, 252 ], 'Rb+' : ['RB', 252],
'Cs+' : [ 'CS', 253, 253 ], 'Cs+' : ['CS', 253],
'Be+' : [ 'BE', 254, 254 ], 'Be+' : ['BE', 254],
'Mg+' : [ 'MG', 255, 2005 ], 'Mg+' : ['MG', 255],
'Ca+' : [ 'CA', 256, 2006 ], 'Ca+' : ['CA', 256],
'Zn+' : [ 'ZN', 257, 257 ], 'Zn+' : ['ZN', 257],
'Cl-' : [ 'Cl', 258, 2007 ] 'Cl-' : ['Cl', 258]
} }
atomTypes = {} atomTypes = {}
...@@ -58,7 +58,6 @@ def getDefaultAtom( ): ...@@ -58,7 +58,6 @@ def getDefaultAtom( ):
atom = dict(); atom = dict();
atom['tinkerLookupName'] = 'XXX' atom['tinkerLookupName'] = 'XXX'
atom['numberOfBonds'] = -1
atom['type'] = -1 atom['type'] = -1
atom['bonds'] = dict() atom['bonds'] = dict()
...@@ -89,7 +88,6 @@ def getXmlAtoms( atoms ): ...@@ -89,7 +88,6 @@ def getXmlAtoms( atoms ):
name = atom.attrib['name'] name = atom.attrib['name']
atomInfo[name] = getDefaultAtom() atomInfo[name] = getDefaultAtom()
atomInfo[name]['tinkerLookupName'] = atom.attrib['tinkerLookupName'] atomInfo[name]['tinkerLookupName'] = atom.attrib['tinkerLookupName']
atomInfo[name]['numberOfBonds'] = atom.attrib['bonds']
return atomInfo return atomInfo
...@@ -113,166 +111,6 @@ def getXmlBonds( bonds ): ...@@ -113,166 +111,6 @@ def getXmlBonds( bonds ):
return bondInfo return bondInfo
#=============================================================================================
# Read residue xml file
#=============================================================================================
def buildResidueDict( residueXmlFileName ):
residueTree = etree.parse(residueXmlFileName)
root = residueTree.getroot()
residueDict = dict()
# residueDict[residueName] = dict()
# ['loc']
# ['type']
# ['atoms'] = dict()
# [atomName] = dict()
# ['bonds'] = dict{}
for residue in root.findall('Residue'):
residueName = residue.attrib['name']
type = residue.attrib['type']
fullName = residue.attrib['fullName']
if( type == 'protein' ):
isProtein = 1
else:
isProtein = 0
bondInfo = getXmlBonds( residue.findall('Bond') )
# if residue is an amino acid, then create CALA and NALA residues, in addition to non-termianal residue, and include approriate atoms
# HXT is excluded from all residues
if( isProtein ):
cResidueName = 'C' + residueName
nResidueName = 'N' + residueName
residueDict[residueName] = dict()
residueDict[cResidueName] = dict()
residueDict[nResidueName] = dict()
residueDict[residueName]['atoms'] = dict()
residueDict[residueName]['type'] = 'protein'
residueDict[residueName]['loc'] = 'middle'
residueDict[residueName]['tinkerLookupName'] = fullName
residueDict[residueName]['fullName'] = fullName
residueDict[residueName]['include'] = 1
residueDict[cResidueName]['atoms'] = dict()
residueDict[cResidueName]['type'] = 'protein'
residueDict[cResidueName]['loc'] = 'C-Terminal'
residueDict[cResidueName]['loc'] = 'C-Terminal'
residueDict[cResidueName]['tinkerLookupName'] = 'C-Terminal ' + residueName
residueDict[cResidueName]['fullName'] = fullName
residueDict[nResidueName]['atoms'] = dict()
residueDict[nResidueName]['type'] = 'protein'
residueDict[nResidueName]['loc'] = 'N-Terminal'
residueDict[cResidueName]['tinkerLookupName'] = 'N-Terminal ' + residueName
residueDict[cResidueName]['fullName'] = fullName
residueList = [ residueDict[residueName]['atoms'], residueDict[cResidueName]['atoms'] , residueDict[nResidueName]['atoms'] ]
for atom in bondInfo:
if( atom == 'OXT' ):
residueDict[cResidueName]['atoms'][atom] = dict()
elif( atom == 'H2' or atom == 'H3'):
residueDict[nResidueName]['atoms'][atom] = dict()
elif( atom != 'HXT' ):
residueDict[nResidueName]['atoms'][atom] = dict()
residueDict[cResidueName]['atoms'][atom] = dict()
residueDict[residueName]['atoms'][atom] = dict()
for atom1 in bondInfo:
for atom2 in bondInfo[atom1]:
for resDict in residueList:
if( atom1 in resDict and atom2 in resDict ):
if( 'bonds' not in resDict[atom1] ):
resDict[atom1]['bonds'] = dict()
if( 'bonds' not in resDict[atom2] ):
resDict[atom2]['bonds'] = dict()
resDict[atom1]['bonds'][atom2] = 1
resDict[atom2]['bonds'][atom1] = 1
else:
residueDict[residueName] = dict()
residueDict[residueName]['atoms'] = dict()
residueDict[residueName]['loc'] = 'unk'
residueDict[residueName]['type'] = 'unk'
residueDict[residueName]['include'] = 0
for atom in bondInfo:
if( atom not in residueDict[residueName]['atoms'] ):
residueDict[residueName]['atoms'][atom] = dict()
residueDict[residueName]['atoms'][atom]['bonds'] = dict()
for atom2 in bondInfo[atom]:
if( atom2 not in residueDict[residueName]['atoms'] ):
residueDict[residueName]['atoms'][atom2] = dict()
residueDict[residueName]['atoms'][atom2]['bonds'] = dict()
residueDict[residueName]['atoms'][atom2]['bonds'][atom] = 1
residueDict[residueName]['atoms'][atom]['bonds'][atom2] = 1
else:
print "File=%s does not have Residues tag." % (residueXmlFileName)
all = list( root.iter() )
for i in all:
print "Tag <%s>" % (i.tag)
etree.dump( root )
printMap = 0
if( printMap ):
print "Residue Map"
for resName in sorted( residueDict.keys() ):
residueInfo = residueDict[resName]['atoms']
print "\nResidue %s %s %s" % (resName, residueDict[resName]['type'], residueDict[resName]['loc'])
for atomName in sorted( residueInfo.keys() ):
bondInfo = residueInfo[atomName]['bonds']
outputString = atomName + ' { '
for bondedAtom in sorted( bondInfo.keys() ):
outputString += bondedAtom + ' '
outputString += ' }'
print "%s" % outputString
print "Start Lookup XML\n\n"
printXml = 1
if( printXml ):
print "<Residues>"
for resName in sorted( residueDict.keys() ):
if( 'include' in residueDict[resName] and residueDict[resName]['include'] ):
type = residueDict[resName]['type']
loc = residueDict[resName]['loc']
tinkerLookupName = residueDict[resName]['tinkerLookupName']
fullName = residueDict[resName]['fullName']
outputString = """ <Residue abbreviation="%s" loc="%s" type="%s" tinkerLookupName="%s" fullName="%s">""" % (resName, loc, type, tinkerLookupName, fullName )
print "%s" % outputString
atomsInfo = residueDict[resName]['atoms']
for atomName in sorted( atomsInfo.keys() ):
numberOfBonds = len( atomsInfo[atomName]['bonds'] )
outputString = """ <Atom name="%s" tinkerLookupName="%s" bonds=%d />""" % (atomName, atomName, numberOfBonds )
print "%s" % outputString
includedBonds = dict()
for atomName in sorted( atomsInfo.keys() ):
bondsInfo = atomsInfo[atomName]['bonds']
for bondedAtom in bondsInfo:
if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ):
outputString = """ <Bond from="%s" to="%s" />""" % (atomName, bondedAtom)
if( atomName not in includedBonds ):
includedBonds[atomName] = dict()
if( bondedAtom not in includedBonds ):
includedBonds[bondedAtom] = dict()
includedBonds[atomName][bondedAtom] = 1
includedBonds[bondedAtom][atomName] = 1
print "%s" % outputString
print "</Residue>"
print "</Residues>"
sys.exit(0)
return residueDict
#============================================================================================= #=============================================================================================
# Build entry for protein residue # Build entry for protein residue
#============================================================================================= #=============================================================================================
...@@ -363,7 +201,7 @@ def copyProteinResidue( residue ): ...@@ -363,7 +201,7 @@ def copyProteinResidue( residue ):
# Build residue hash based on xml file # Build residue hash based on xml file
#============================================================================================= #=============================================================================================
def buildResidueDictFinal( residueXmlFileName ): def buildResidueDict( residueXmlFileName ):
residueTree = etree.parse(residueXmlFileName) residueTree = etree.parse(residueXmlFileName)
print "Read %s" % (residueXmlFileName) print "Read %s" % (residueXmlFileName)
...@@ -384,12 +222,18 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -384,12 +222,18 @@ def buildResidueDictFinal( residueXmlFileName ):
type = residue.attrib['type'] type = residue.attrib['type']
tinkerName = residue.attrib['tinkerLookupName'] tinkerName = residue.attrib['tinkerLookupName']
residueName = residue.attrib['fullName'] residueName = residue.attrib['fullName']
isProtein = 0 isProtein = False
isWater = 0 isWater = False
if( type == 'protein' ): isDNA = False
isProtein = 1 isRNA = False
elif( type == 'AmoebaWater' ): if type == 'protein':
isWater = 1 isProtein = True
elif type == 'AmoebaWater':
isWater = True
elif type == 'dna':
isDNA = True
elif type == 'rna':
isRNA = True
else: else:
continue continue
...@@ -448,6 +292,10 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -448,6 +292,10 @@ def buildResidueDictFinal( residueXmlFileName ):
residueDict[nResidueName]['atoms']['H2'] = copyAtom( residueDict[abbr]['atoms']['H'] ) residueDict[nResidueName]['atoms']['H2'] = copyAtom( residueDict[abbr]['atoms']['H'] )
residueDict[nResidueName]['atoms']['H3'] = copyAtom( residueDict[abbr]['atoms']['H'] ) residueDict[nResidueName]['atoms']['H3'] = copyAtom( residueDict[abbr]['atoms']['H'] )
elif isDNA or isRNA:
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 printXml = 1
if( printXml ): if( printXml ):
...@@ -463,9 +311,8 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -463,9 +311,8 @@ def buildResidueDictFinal( residueXmlFileName ):
atomsInfo = residueDict[resName]['atoms'] atomsInfo = residueDict[resName]['atoms']
for atomName in sorted( atomsInfo.keys() ): for atomName in sorted( atomsInfo.keys() ):
numberOfBonds = atomsInfo[atomName]['numberOfBonds']
tinkerLookupName = atomsInfo[atomName]['tinkerLookupName'] tinkerLookupName = atomsInfo[atomName]['tinkerLookupName']
outputString = """ <Atom name="%s" tinkerLookupName="%s" bonds="%s" />""" % (atomName, tinkerLookupName, numberOfBonds ) outputString = """ <Atom name="%s" tinkerLookupName="%s" />""" % (atomName, tinkerLookupName)
print "%s" % outputString print "%s" % outputString
includedBonds = dict() includedBonds = dict()
...@@ -492,18 +339,35 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -492,18 +339,35 @@ def buildResidueDictFinal( residueXmlFileName ):
def setBioTypes( bioTypes, residueDict ): def setBioTypes( bioTypes, residueDict ):
for res in residueDict: for resname, res in residueDict.items():
for atom in residueDict[res]['atoms']: for atom in res['atoms']:
lookupName = residueDict[res]['atoms'][atom]['tinkerLookupName'] + '_' + residueDict[res]['tinkerLookupName'] atomLookup = res['atoms'][atom]['tinkerLookupName']
if( lookupName in bioTypes ): resLookup = []
residueDict[res]['atoms'][atom]['type'] = bioTypes[lookupName][3] if res['type'] == 'dna':
if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl DNA")
if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl DNA")
resLookup.append("Phosphodiester DNA")
if res['type'] == 'rna':
if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl RNA")
if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl RNA")
resLookup.append("Phosphodiester RNA")
resLookup.append(res['tinkerLookupName'])
for suffix in resLookup:
lookupName = atomLookup+'_'+suffix
if lookupName in bioTypes:
break
if lookupName in bioTypes:
res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else: else:
print "For %s lookupName=%s not in biotype" % (atom,lookupName) print "For %s lookupName=%s not in biotype" % (atom,lookupName)
if( 'parent' in residueDict[res] ): if( 'parent' in res ):
lookupName = residueDict[res]['atoms'][atom]['tinkerLookupName'] + '_' + residueDict[res]['parent']['tinkerLookupName'] lookupName = res['atoms'][atom]['tinkerLookupName'] + '_' + res['parent']['tinkerLookupName']
if( lookupName in bioTypes ): if( lookupName in bioTypes ):
residueDict[res]['atoms'][atom]['type'] = bioTypes[lookupName][3] res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else: else:
print "Missing lookupName=%s from biotype" % (lookupName) print "Missing lookupName=%s from biotype" % (lookupName)
return 0 return 0
...@@ -584,14 +448,8 @@ def addTorTor( lineIndex, allLines, forces ): ...@@ -584,14 +448,8 @@ def addTorTor( lineIndex, allLines, forces ):
#============================================================================================= #=============================================================================================
old = 0 residueXmlFileName = 'residuesFinal.xml'
if( old ): residueDict = buildResidueDict( residueXmlFileName )
residueXmlFileName = '/home/friedrim/source/pyTinker/residues.xml'
residueXmlFileName = '/home/friedrim/source/pyTinker/residues.xml'
residueDict = buildResidueDict( residueXmlFileName )
else:
residueXmlFileName = 'residuesFinal.xml'
residueDict = buildResidueDictFinal( residueXmlFileName )
#============================================================================================= #=============================================================================================
...@@ -687,6 +545,7 @@ while lineIndex < len( allLines ): ...@@ -687,6 +545,7 @@ while lineIndex < len( allLines ):
if( fields[3] in ions ): if( fields[3] in ions ):
ionInfo = ions[fields[3]] ionInfo = ions[fields[3]]
element = ionInfo[0] element = ionInfo[0]
ionInfo[1] = int(fields[1])
else: else:
element = fields[3][0] element = fields[3][0]
atomTypes[int(fields[1])] = (fields[2], element, fields[6]) atomTypes[int(fields[1])] = (fields[2], element, fields[6])
...@@ -695,6 +554,9 @@ while lineIndex < len( allLines ): ...@@ -695,6 +554,9 @@ while lineIndex < len( allLines ):
elif fields[0] == 'biotype': elif fields[0] == 'biotype':
lookUp = fields[2] + '_' + fields[3] lookUp = fields[2] + '_' + fields[3]
if lookUp in bioTypes:
# Workaround for Tinker using the same name but different types for H2', H2'', and for H5', H5''
lookUp = fields[2]+'*_'+fields[3]
bioTypes[lookUp] = fields[1:] bioTypes[lookUp] = fields[1:]
lineIndex += 1 lineIndex += 1
...@@ -736,12 +598,17 @@ print "Opened %s." % (gkXmlFileName) ...@@ -736,12 +598,17 @@ print "Opened %s." % (gkXmlFileName)
today = datetime.date.today().isoformat() today = datetime.date.today().isoformat()
sourceFile = os.path.basename(sys.argv[1]) sourceFile = os.path.basename(sys.argv[1])
header = "<!-- Generated on %s from %s -->\n\n" % (today, sourceFile) header = """ <Info>
tinkerXmlFile.write(header) <Source>%s</Source>
gkXmlFile.write(header) <DateGenerated>%s</DateGenerated>
<Reference></Reference>
</Info>
""" % (sourceFile, today)
gkXmlFile.write( "<ForceField>\n" ) gkXmlFile.write( "<ForceField>\n" )
gkXmlFile.write(header)
tinkerXmlFile.write( "<ForceField>\n" ) tinkerXmlFile.write( "<ForceField>\n" )
tinkerXmlFile.write(header)
tinkerXmlFile.write( " <AtomTypes>\n") tinkerXmlFile.write( " <AtomTypes>\n")
if( scalars['forcefield'].find( 'AMOEBA' ) > -1 ): if( scalars['forcefield'].find( 'AMOEBA' ) > -1 ):
...@@ -803,25 +670,25 @@ tinkerXmlFile.write( " </AtomTypes>\n") ...@@ -803,25 +670,25 @@ tinkerXmlFile.write( " </AtomTypes>\n")
# residues # residues
tinkerXmlFile.write( " <Residues>\n" ) tinkerXmlFile.write( " <Residues>\n" )
for res in sorted(residueDict): for resname, res in sorted(residueDict.items()):
if( residueDict[res]['include'] ): if res['include']:
outputString = """ <Residue name="%s">""" % (res) outputString = """ <Residue name="%s">""" % (resname)
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
atomIndex = dict() atomIndex = dict()
atomCount = 0 atomCount = 0
for atom in sorted( residueDict[res]['atoms'].keys() ): for atom in sorted( res['atoms'].keys() ):
type = residueDict[res]['atoms'][atom]['type'] type = res['atoms'][atom]['type']
typeI = int( type ) typeI = int( type )
if( typeI < 0 ): if( typeI < 0 ):
print "Error: type=%s for atom=%s of residue=%s" % (type, atom, res) print "Error: type=%s for atom=%s of residue=%s" % (type, atom, resname)
tag = " <Atom name=\"%s\" type=\"%s\" />" % (atom, type) tag = " <Atom name=\"%s\" type=\"%s\" />" % (atom, type)
atomIndex[atom] = atomCount atomIndex[atom] = atomCount
atomCount += 1 atomCount += 1
tinkerXmlFile.write( "%s\n" % (tag) ) tinkerXmlFile.write( "%s\n" % (tag) )
includedBonds = dict() includedBonds = dict()
for atomName in sorted( residueDict[res]['atoms'].keys() ): for atomName in sorted( res['atoms'].keys() ):
bondsInfo = residueDict[res]['atoms'][atomName]['bonds'] bondsInfo = res['atoms'][atomName]['bonds']
for bondedAtom in bondsInfo: for bondedAtom in bondsInfo:
if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ): if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ):
outputString = """ <Bond from="%s" to="%s" />""" % (str(atomIndex[atomName]), str(atomIndex[bondedAtom])) outputString = """ <Bond from="%s" to="%s" />""" % (str(atomIndex[atomName]), str(atomIndex[bondedAtom]))
...@@ -834,15 +701,21 @@ for res in sorted(residueDict): ...@@ -834,15 +701,21 @@ for res in sorted(residueDict):
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
outputStrings = [] outputStrings = []
if( residueDict[res]['loc'] == 'm' ): if res['type'] in ('rna', 'dna'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) )) if res['loc'] in ('middle', '3'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['P']) ))
if( residueDict[res]['loc'] == 'n' ): if res['loc'] in ('middle', '5'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex["O3'"]) ))
if( residueDict[res]['loc'] == 'c' ): else:
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ) ) if res['loc'] == 'm':
if( res.find('CYX') > -1 ): outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ))
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['SG']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) )
if res['loc'] == 'n':
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) )
if res['loc'] == 'c':
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ) )
if resname.find('CYX') > -1:
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['SG']) ) )
for outputString in outputStrings: for outputString in outputStrings:
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
...@@ -960,24 +833,26 @@ if( isAmoeba ): ...@@ -960,24 +833,26 @@ if( isAmoeba ):
# AmoebaTorsionForce # AmoebaTorsionForce
torsionUnit = float(scalars['torsionunit']) torsionUnit = float(scalars['torsionunit'])
outputString = """ <AmoebaTorsionForce torsionUnit="%s">""" % ( torsionUnit ) outputString = """ <PeriodicTorsionForce>"""
tinkerXmlFile.write( "%s\n" % (outputString ) ) tinkerXmlFile.write( "%s\n" % (outputString ) )
torsions = forces['torsion'] torsions = forces['torsion']
conversion = 4.184*torsionUnit conversion = 4.184*torsionUnit
for torsion in torsions: for torsion in torsions:
outputString = """ <Torsion class1="%s" class2="%s" class3="%s" class4="%s" """ % (torsion[0], torsion[1], torsion[2], torsion[3]) outputString = """ <Proper class1="%s" class2="%s" class3="%s" class4="%s" """ % (torsion[0], torsion[1], torsion[2], torsion[3])
startIndex = 4 startIndex = 4
for ii in range(0,3): for ii in range(0,3):
torsionSuffix = str(ii+1) torsionSuffix = str(ii+1)
amplitudeAttributeName = 'amp' + torsionSuffix amplitudeAttributeName = 'k'+torsionSuffix
angleAttributeName = 'angle' + torsionSuffix angleAttributeName = 'phase'+torsionSuffix
periodicityAttributeName = 'periodicity'+torsionSuffix
amplitude = float(torsion[startIndex])*conversion amplitude = float(torsion[startIndex])*conversion
angle = float(torsion[startIndex+1])/radian angle = float(torsion[startIndex+1])/radian
outputString += """ %s="%s" %s="%s" """ % (amplitudeAttributeName, str(amplitude), angleAttributeName, str(angle) ) periodicity = int(torsion[startIndex+2])
outputString += """ %s="%s" %s="%s" %s="%s" """ % (amplitudeAttributeName, str(amplitude), angleAttributeName, str(angle), periodicityAttributeName, str(periodicity))
startIndex += 3 startIndex += 3
outputString += "/>" outputString += "/>"
tinkerXmlFile.write( "%s\n" % (outputString ) ) tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaTorsionForce>\n" ) tinkerXmlFile.write( " </PeriodicTorsionForce>\n" )
#============================================================================================= #=============================================================================================
...@@ -1162,7 +1037,7 @@ if( isAmoeba ): ...@@ -1162,7 +1037,7 @@ if( isAmoeba ):
# radii are set in forcefield.py # radii are set in forcefield.py
for type in sorted( atomTypes ): for type in sorted( atomTypes ):
print "atoom type=%s %s" % ( str(type), str(atomTypes[type]) ) print "atom type=%s %s" % ( str(type), str(atomTypes[type]) )
for type in sorted( bioTypes ): 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]) )
......
devtools/forcefield-scripts/residuesFinal.xml
View file @ 4d32047c
...@@ -942,4 +942,2124 @@ ...@@ -942,4 +942,2124 @@
<Bond from="CG2" to="HG22" /> <Bond from="CG2" to="HG22" />
<Bond from="H" to="N" /> <Bond from="H" to="N" />
</Residue> </Residue>
<Residue abbreviation="DA" loc="middle" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DA3" loc="3" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DA5" loc="5" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DAN" loc="N" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DC" loc="middle" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DC3" loc="3" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DC5" loc="5" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DCN" loc="N" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DG" loc="middle" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DG3" loc="3" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DG5" loc="5" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DGN" loc="N" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DT" loc="middle" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DT3" loc="3" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DT5" loc="5" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DTN" loc="N" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RA" loc="middle" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RA3" loc="3" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RA5" loc="5" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RAN" loc="N" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RC" loc="middle" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RC3" loc="3" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RC5" loc="5" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RCN" loc="N" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RG" loc="middle" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RG3" loc="3" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RG5" loc="5" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RGN" loc="N" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RU" loc="middle" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RU3" loc="3" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RU5" loc="5" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RUN" loc="N" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
</Residues> </Residues>
wrappers/python/simtk/openmm/app/data/amoeba2009.xml
View file @ 4d32047c
This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/simtk/openmm/app/data/amoeba2009_gk.xml
View file @ 4d32047c
<ForceField> <ForceField>
<AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" dielectricOffset="0.009" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663"> <Info>
<GeneralizedKirkwood type="1" charge="-0.22620" shct="0.79" /> <Source>amoebabio09.prm</Source>
<GeneralizedKirkwood type="2" charge="-0.15245" shct="0.72" /> <DateGenerated>2015-11-19</DateGenerated>
<GeneralizedKirkwood type="2" charge="-0.26188" shct="0.72" /> <Reference></Reference>
<GeneralizedKirkwood type="2" charge="-0.00060" shct="0.72" /> </Info>
<GeneralizedKirkwood type="3" charge="0.84374" shct="0.72" /> <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
<GeneralizedKirkwood type="4" charge="0.12752" shct="0.85" /> <GeneralizedKirkwood type="1" charge="-0.22620" shct="0.79" />
<GeneralizedKirkwood type="5" charge="-0.73597" shct="0.85" /> <GeneralizedKirkwood type="2" charge="-0.15245" shct="0.72" />
<GeneralizedKirkwood type="6" charge="0.07168" shct="0.85" /> <GeneralizedKirkwood type="2" charge="-0.26188" shct="0.72" />
<GeneralizedKirkwood type="7" charge="-0.14985" shct="0.79" /> <GeneralizedKirkwood type="2" charge="-0.06378" shct="0.72" />
<GeneralizedKirkwood type="7" charge="-0.07700" shct="0.79" /> <GeneralizedKirkwood type="2" charge="-0.00060" shct="0.72" />
<GeneralizedKirkwood type="7" charge="-0.14168" shct="0.79" /> <GeneralizedKirkwood type="2" charge="-0.15431" shct="0.72" />
<GeneralizedKirkwood type="8" charge="-0.21238" shct="0.72" /> <GeneralizedKirkwood type="3" charge="0.84374" shct="0.72" />
<GeneralizedKirkwood type="8" charge="-0.35660" shct="0.72" /> <GeneralizedKirkwood type="4" charge="0.12752" shct="0.85" />
<GeneralizedKirkwood type="8" charge="0.01822" shct="0.72" /> <GeneralizedKirkwood type="5" charge="-0.73597" shct="0.85" />
<GeneralizedKirkwood type="9" charge="0.85068" shct="0.72" /> <GeneralizedKirkwood type="6" charge="0.07168" shct="0.85" />
<GeneralizedKirkwood type="9" charge="0.86830" shct="0.72" /> <GeneralizedKirkwood type="7" charge="-0.14985" shct="0.79" />
<GeneralizedKirkwood type="9" charge="0.86623" shct="0.72" /> <GeneralizedKirkwood type="7" charge="-0.07700" shct="0.79" />
<GeneralizedKirkwood type="10" charge="0.12992" shct="0.85" /> <GeneralizedKirkwood type="7" charge="-0.14168" shct="0.79" />
<GeneralizedKirkwood type="10" charge="0.13014" shct="0.85" /> <GeneralizedKirkwood type="8" charge="-0.21238" shct="0.72" />
<GeneralizedKirkwood type="10" charge="0.13192" shct="0.85" /> <GeneralizedKirkwood type="8" charge="-0.35660" shct="0.72" />
<GeneralizedKirkwood type="11" charge="-0.77770" shct="0.85" /> <GeneralizedKirkwood type="8" charge="-0.15850" shct="0.72" />
<GeneralizedKirkwood type="11" charge="-0.78568" shct="0.85" /> <GeneralizedKirkwood type="8" charge="0.01822" shct="0.72" />
<GeneralizedKirkwood type="11" charge="-0.77214" shct="0.85" /> <GeneralizedKirkwood type="8" charge="-0.13549" shct="0.72" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="9" charge="0.85068" shct="0.72" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="9" charge="0.86830" shct="0.72" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="9" charge="0.86623" shct="0.72" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="10" charge="0.12992" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="10" charge="0.13014" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="10" charge="0.13192" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="11" charge="-0.77770" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="11" charge="-0.78568" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="11" charge="-0.77214" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08544" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08646" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.09030" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.08972" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.09885" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="12" charge="0.09273" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="13" charge="-0.15440" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="14" charge="0.07484" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="15" charge="0.01482" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="16" charge="0.06618" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08921" shct="0.85" />
<GeneralizedKirkwood type="17" charge="-0.17773" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.08544" shct="0.85" />
<GeneralizedKirkwood type="18" charge="0.05743" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.08646" shct="0.85" />
<GeneralizedKirkwood type="19" charge="-0.05880" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.09030" shct="0.85" />
<GeneralizedKirkwood type="21" charge="0.02425" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.08972" shct="0.85" />
<GeneralizedKirkwood type="23" charge="-0.11850" shct="0.72" /> <GeneralizedKirkwood type="12" charge="0.09885" shct="0.85" />
<GeneralizedKirkwood type="20" charge="0.04696" shct="0.85" /> <GeneralizedKirkwood type="12" charge="0.09273" shct="0.85" />
<GeneralizedKirkwood type="22" charge="0.00841" shct="0.85" /> <GeneralizedKirkwood type="13" charge="-0.15440" shct="0.72" />
<GeneralizedKirkwood type="24" charge="0.03989" shct="0.85" /> <GeneralizedKirkwood type="14" charge="0.07484" shct="0.85" />
<GeneralizedKirkwood type="25" charge="0.02186" shct="0.72" /> <GeneralizedKirkwood type="15" charge="0.01482" shct="0.72" />
<GeneralizedKirkwood type="26" charge="0.06618" shct="0.85" /> <GeneralizedKirkwood type="16" charge="0.06618" shct="0.85" />
<GeneralizedKirkwood type="27" charge="-0.17773" shct="0.72" /> <GeneralizedKirkwood type="17" charge="-0.17773" shct="0.72" />
<GeneralizedKirkwood type="28" charge="0.05743" shct="0.85" /> <GeneralizedKirkwood type="18" charge="0.05743" shct="0.85" />
<GeneralizedKirkwood type="29" charge="-0.13782" shct="0.72" /> <GeneralizedKirkwood type="19" charge="-0.05880" shct="0.72" />
<GeneralizedKirkwood type="30" charge="0.05838" shct="0.85" /> <GeneralizedKirkwood type="21" charge="0.02425" shct="0.72" />
<GeneralizedKirkwood type="31" charge="-0.16689" shct="0.72" /> <GeneralizedKirkwood type="23" charge="-0.11850" shct="0.72" />
<GeneralizedKirkwood type="32" charge="0.05849" shct="0.85" /> <GeneralizedKirkwood type="20" charge="0.04696" shct="0.85" />
<GeneralizedKirkwood type="33" charge="-0.31424" shct="0.72" /> <GeneralizedKirkwood type="22" charge="0.00841" shct="0.85" />
<GeneralizedKirkwood type="33" charge="-0.44882" shct="0.72" /> <GeneralizedKirkwood type="24" charge="0.03989" shct="0.85" />
<GeneralizedKirkwood type="33" charge="-0.01057" shct="0.72" /> <GeneralizedKirkwood type="25" charge="0.02186" shct="0.72" />
<GeneralizedKirkwood type="34" charge="0.18740" shct="0.72" /> <GeneralizedKirkwood type="26" charge="0.06618" shct="0.85" />
<GeneralizedKirkwood type="35" charge="0.01982" shct="0.85" /> <GeneralizedKirkwood type="27" charge="-0.17773" shct="0.72" />
<GeneralizedKirkwood type="36" charge="-0.41295" shct="0.85" /> <GeneralizedKirkwood type="28" charge="0.05743" shct="0.85" />
<GeneralizedKirkwood type="37" charge="0.27409" shct="0.85" /> <GeneralizedKirkwood type="29" charge="-0.13782" shct="0.72" />
<GeneralizedKirkwood type="38" charge="0.17854" shct="0.72" /> <GeneralizedKirkwood type="30" charge="0.05838" shct="0.85" />
<GeneralizedKirkwood type="39" charge="0.02134" shct="0.85" /> <GeneralizedKirkwood type="31" charge="-0.16689" shct="0.72" />
<GeneralizedKirkwood type="40" charge="-0.15307" shct="0.72" /> <GeneralizedKirkwood type="32" charge="0.05849" shct="0.85" />
<GeneralizedKirkwood type="41" charge="0.07192" shct="0.85" /> <GeneralizedKirkwood type="33" charge="-0.31424" shct="0.72" />
<GeneralizedKirkwood type="42" charge="-0.39938" shct="0.85" /> <GeneralizedKirkwood type="33" charge="-0.44882" shct="0.72" />
<GeneralizedKirkwood type="43" charge="0.22557" shct="0.85" /> <GeneralizedKirkwood type="33" charge="-0.01057" shct="0.72" />
<GeneralizedKirkwood type="44" charge="-0.24710" shct="0.72" /> <GeneralizedKirkwood type="33" charge="-0.16428" shct="0.72" />
<GeneralizedKirkwood type="44" charge="-0.37021" shct="0.72" /> <GeneralizedKirkwood type="34" charge="0.18740" shct="0.72" />
<GeneralizedKirkwood type="44" charge="-0.00633" shct="0.72" /> <GeneralizedKirkwood type="35" charge="0.01982" shct="0.85" />
<GeneralizedKirkwood type="45" charge="-0.15207" shct="0.72" /> <GeneralizedKirkwood type="36" charge="-0.41295" shct="0.85" />
<GeneralizedKirkwood type="45" charge="-0.15207" shct="0.72" /> <GeneralizedKirkwood type="37" charge="0.27409" shct="0.85" />
<GeneralizedKirkwood type="46" charge="0.07591" shct="0.85" /> <GeneralizedKirkwood type="38" charge="0.17854" shct="0.72" />
<GeneralizedKirkwood type="47" charge="-0.04712" shct="0.96" /> <GeneralizedKirkwood type="39" charge="0.02134" shct="0.85" />
<GeneralizedKirkwood type="48" charge="0.11129" shct="0.85" /> <GeneralizedKirkwood type="40" charge="-0.15307" shct="0.72" />
<GeneralizedKirkwood type="49" charge="0.06417" shct="0.96" /> <GeneralizedKirkwood type="41" charge="0.07192" shct="0.85" />
<GeneralizedKirkwood type="50" charge="0.02101" shct="0.72" /> <GeneralizedKirkwood type="42" charge="-0.39938" shct="0.85" />
<GeneralizedKirkwood type="51" charge="0.00952" shct="0.85" /> <GeneralizedKirkwood type="43" charge="0.22557" shct="0.85" />
<GeneralizedKirkwood type="52" charge="-0.97001" shct="0.96" /> <GeneralizedKirkwood type="44" charge="-0.24710" shct="0.72" />
<GeneralizedKirkwood type="53" charge="-0.11893" shct="0.79" /> <GeneralizedKirkwood type="44" charge="-0.37021" shct="0.72" />
<GeneralizedKirkwood type="54" charge="-0.38385" shct="0.72" /> <GeneralizedKirkwood type="44" charge="-0.00633" shct="0.72" />
<GeneralizedKirkwood type="54" charge="-0.44047" shct="0.72" /> <GeneralizedKirkwood type="44" charge="-0.16004" shct="0.72" />
<GeneralizedKirkwood type="55" charge="0.98874" shct="0.72" /> <GeneralizedKirkwood type="45" charge="-0.15207" shct="0.72" />
<GeneralizedKirkwood type="56" charge="-0.82816" shct="0.85" /> <GeneralizedKirkwood type="45" charge="-0.15207" shct="0.72" />
<GeneralizedKirkwood type="57" charge="0.10715" shct="0.85" /> <GeneralizedKirkwood type="46" charge="0.07591" shct="0.85" />
<GeneralizedKirkwood type="58" charge="-0.09495" shct="0.72" /> <GeneralizedKirkwood type="47" charge="-0.04712" shct="0.96" />
<GeneralizedKirkwood type="58" charge="-0.12680" shct="0.72" /> <GeneralizedKirkwood type="48" charge="0.11129" shct="0.85" />
<GeneralizedKirkwood type="59" charge="0.09275" shct="0.85" /> <GeneralizedKirkwood type="49" charge="0.06417" shct="0.96" />
<GeneralizedKirkwood type="59" charge="0.11510" shct="0.85" /> <GeneralizedKirkwood type="50" charge="0.02101" shct="0.72" />
<GeneralizedKirkwood type="60" charge="-0.11624" shct="0.72" /> <GeneralizedKirkwood type="51" charge="0.00952" shct="0.85" />
<GeneralizedKirkwood type="60" charge="-0.14420" shct="0.72" /> <GeneralizedKirkwood type="52" charge="-0.97001" shct="0.96" />
<GeneralizedKirkwood type="61" charge="0.09217" shct="0.85" /> <GeneralizedKirkwood type="53" charge="-0.11893" shct="0.79" />
<GeneralizedKirkwood type="61" charge="0.12121" shct="0.85" /> <GeneralizedKirkwood type="54" charge="-0.38385" shct="0.72" />
<GeneralizedKirkwood type="62" charge="-0.02016" shct="0.72" /> <GeneralizedKirkwood type="54" charge="-0.44047" shct="0.72" />
<GeneralizedKirkwood type="63" charge="0.04828" shct="0.85" /> <GeneralizedKirkwood type="55" charge="0.98874" shct="0.72" />
<GeneralizedKirkwood type="64" charge="-0.01895" shct="0.72" /> <GeneralizedKirkwood type="56" charge="-0.82816" shct="0.85" />
<GeneralizedKirkwood type="65" charge="0.06839" shct="0.85" /> <GeneralizedKirkwood type="57" charge="0.10715" shct="0.85" />
<GeneralizedKirkwood type="66" charge="-0.06275" shct="0.72" /> <GeneralizedKirkwood type="58" charge="-0.09495" shct="0.72" />
<GeneralizedKirkwood type="67" charge="0.00890" shct="0.72" /> <GeneralizedKirkwood type="58" charge="-0.12680" shct="0.72" />
<GeneralizedKirkwood type="68" charge="0.02818" shct="0.85" /> <GeneralizedKirkwood type="59" charge="0.09275" shct="0.85" />
<GeneralizedKirkwood type="69" charge="-0.05402" shct="0.72" /> <GeneralizedKirkwood type="59" charge="0.11510" shct="0.85" />
<GeneralizedKirkwood type="70" charge="0.03565" shct="0.85" /> <GeneralizedKirkwood type="60" charge="-0.11624" shct="0.72" />
<GeneralizedKirkwood type="71" charge="-0.05826" shct="0.72" /> <GeneralizedKirkwood type="60" charge="-0.14420" shct="0.72" />
<GeneralizedKirkwood type="72" charge="0.03588" shct="0.85" /> <GeneralizedKirkwood type="61" charge="0.09217" shct="0.85" />
<GeneralizedKirkwood type="73" charge="-0.08206" shct="0.72" /> <GeneralizedKirkwood type="61" charge="0.12121" shct="0.85" />
<GeneralizedKirkwood type="74" charge="0.09740" shct="0.85" /> <GeneralizedKirkwood type="62" charge="-0.02016" shct="0.72" />
<GeneralizedKirkwood type="75" charge="-0.04596" shct="0.72" /> <GeneralizedKirkwood type="63" charge="0.04828" shct="0.85" />
<GeneralizedKirkwood type="76" charge="0.05037" shct="0.72" /> <GeneralizedKirkwood type="64" charge="-0.01895" shct="0.72" />
<GeneralizedKirkwood type="77" charge="0.01064" shct="0.85" /> <GeneralizedKirkwood type="65" charge="0.06839" shct="0.85" />
<GeneralizedKirkwood type="78" charge="-0.12462" shct="0.72" /> <GeneralizedKirkwood type="66" charge="-0.06275" shct="0.72" />
<GeneralizedKirkwood type="79" charge="0.01162" shct="0.85" /> <GeneralizedKirkwood type="67" charge="0.00890" shct="0.72" />
<GeneralizedKirkwood type="80" charge="0.34249" shct="0.72" /> <GeneralizedKirkwood type="68" charge="0.02818" shct="0.85" />
<GeneralizedKirkwood type="81" charge="-0.46444" shct="0.85" /> <GeneralizedKirkwood type="69" charge="-0.05402" shct="0.72" />
<GeneralizedKirkwood type="82" charge="0.22927" shct="0.85" /> <GeneralizedKirkwood type="70" charge="0.03565" shct="0.85" />
<GeneralizedKirkwood type="83" charge="-0.14811" shct="0.72" /> <GeneralizedKirkwood type="71" charge="-0.05826" shct="0.72" />
<GeneralizedKirkwood type="84" charge="0.08044" shct="0.85" /> <GeneralizedKirkwood type="72" charge="0.03588" shct="0.85" />
<GeneralizedKirkwood type="85" charge="-0.21500" shct="0.72" /> <GeneralizedKirkwood type="73" charge="-0.08206" shct="0.72" />
<GeneralizedKirkwood type="86" charge="-0.04459" shct="0.72" /> <GeneralizedKirkwood type="74" charge="0.09740" shct="0.85" />
<GeneralizedKirkwood type="87" charge="0.01849" shct="0.85" /> <GeneralizedKirkwood type="75" charge="-0.04596" shct="0.72" />
<GeneralizedKirkwood type="88" charge="-0.15802" shct="0.72" /> <GeneralizedKirkwood type="76" charge="0.05037" shct="0.72" />
<GeneralizedKirkwood type="89" charge="-0.03234" shct="0.85" /> <GeneralizedKirkwood type="77" charge="0.01064" shct="0.85" />
<GeneralizedKirkwood type="90" charge="0.62054" shct="0.72" /> <GeneralizedKirkwood type="78" charge="-0.12462" shct="0.72" />
<GeneralizedKirkwood type="91" charge="-0.91150" shct="0.85" /> <GeneralizedKirkwood type="79" charge="0.01162" shct="0.85" />
<GeneralizedKirkwood type="92" charge="-0.16392" shct="0.72" /> <GeneralizedKirkwood type="80" charge="0.34249" shct="0.72" />
<GeneralizedKirkwood type="93" charge="0.09307" shct="0.85" /> <GeneralizedKirkwood type="81" charge="-0.46444" shct="0.85" />
<GeneralizedKirkwood type="94" charge="-0.10518" shct="0.72" /> <GeneralizedKirkwood type="82" charge="0.22927" shct="0.85" />
<GeneralizedKirkwood type="95" charge="0.06363" shct="0.72" /> <GeneralizedKirkwood type="83" charge="-0.14811" shct="0.72" />
<GeneralizedKirkwood type="96" charge="0.02858" shct="0.85" /> <GeneralizedKirkwood type="84" charge="0.08044" shct="0.85" />
<GeneralizedKirkwood type="97" charge="0.00670" shct="0.72" /> <GeneralizedKirkwood type="85" charge="-0.21500" shct="0.72" />
<GeneralizedKirkwood type="98" charge="-0.04014" shct="0.79" /> <GeneralizedKirkwood type="86" charge="-0.04459" shct="0.72" />
<GeneralizedKirkwood type="99" charge="0.08943" shct="0.85" /> <GeneralizedKirkwood type="87" charge="0.01849" shct="0.85" />
<GeneralizedKirkwood type="100" charge="0.27213" shct="0.72" /> <GeneralizedKirkwood type="88" charge="-0.15802" shct="0.72" />
<GeneralizedKirkwood type="101" charge="-0.21794" shct="0.72" /> <GeneralizedKirkwood type="89" charge="-0.03234" shct="0.85" />
<GeneralizedKirkwood type="102" charge="0.00801" shct="0.85" /> <GeneralizedKirkwood type="90" charge="0.62054" shct="0.72" />
<GeneralizedKirkwood type="103" charge="-0.11761" shct="0.72" /> <GeneralizedKirkwood type="91" charge="-0.91150" shct="0.85" />
<GeneralizedKirkwood type="104" charge="0.00440" shct="0.85" /> <GeneralizedKirkwood type="92" charge="-0.16392" shct="0.72" />
<GeneralizedKirkwood type="105" charge="0.10201" shct="0.72" /> <GeneralizedKirkwood type="93" charge="0.09307" shct="0.85" />
<GeneralizedKirkwood type="106" charge="0.00775" shct="0.85" /> <GeneralizedKirkwood type="94" charge="-0.10518" shct="0.72" />
<GeneralizedKirkwood type="107" charge="-0.05764" shct="0.72" /> <GeneralizedKirkwood type="95" charge="0.06363" shct="0.72" />
<GeneralizedKirkwood type="108" charge="0.00377" shct="0.85" /> <GeneralizedKirkwood type="96" charge="0.02858" shct="0.85" />
<GeneralizedKirkwood type="109" charge="-0.04139" shct="0.72" /> <GeneralizedKirkwood type="97" charge="0.00670" shct="0.72" />
<GeneralizedKirkwood type="110" charge="0.12549" shct="0.85" /> <GeneralizedKirkwood type="98" charge="-0.04014" shct="0.79" />
<GeneralizedKirkwood type="111" charge="0.11571" shct="0.72" /> <GeneralizedKirkwood type="99" charge="0.08943" shct="0.85" />
<GeneralizedKirkwood type="112" charge="-0.06925" shct="0.79" /> <GeneralizedKirkwood type="100" charge="0.27213" shct="0.72" />
<GeneralizedKirkwood type="113" charge="0.21415" shct="0.85" /> <GeneralizedKirkwood type="101" charge="-0.21794" shct="0.72" />
<GeneralizedKirkwood type="114" charge="0.01888" shct="0.72" /> <GeneralizedKirkwood type="102" charge="0.00801" shct="0.85" />
<GeneralizedKirkwood type="115" charge="0.06585" shct="0.85" /> <GeneralizedKirkwood type="103" charge="-0.11761" shct="0.72" />
<GeneralizedKirkwood type="116" charge="0.36202" shct="0.72" /> <GeneralizedKirkwood type="104" charge="0.00440" shct="0.85" />
<GeneralizedKirkwood type="117" charge="0.08951" shct="0.85" /> <GeneralizedKirkwood type="105" charge="0.10201" shct="0.72" />
<GeneralizedKirkwood type="118" charge="-0.07427" shct="0.79" /> <GeneralizedKirkwood type="106" charge="0.00775" shct="0.85" />
<GeneralizedKirkwood type="119" charge="0.13793" shct="0.85" /> <GeneralizedKirkwood type="107" charge="-0.05764" shct="0.72" />
<GeneralizedKirkwood type="120" charge="-0.07944" shct="0.72" /> <GeneralizedKirkwood type="108" charge="0.00377" shct="0.85" />
<GeneralizedKirkwood type="121" charge="0.08230" shct="0.85" /> <GeneralizedKirkwood type="109" charge="-0.04139" shct="0.72" />
<GeneralizedKirkwood type="122" charge="0.02915" shct="0.72" /> <GeneralizedKirkwood type="110" charge="0.12549" shct="0.85" />
<GeneralizedKirkwood type="123" charge="-0.20791" shct="0.79" /> <GeneralizedKirkwood type="111" charge="0.11571" shct="0.72" />
<GeneralizedKirkwood type="124" charge="0.22642" shct="0.85" /> <GeneralizedKirkwood type="112" charge="-0.06925" shct="0.79" />
<GeneralizedKirkwood type="125" charge="0.02645" shct="0.72" /> <GeneralizedKirkwood type="113" charge="0.21415" shct="0.85" />
<GeneralizedKirkwood type="126" charge="0.05039" shct="0.85" /> <GeneralizedKirkwood type="114" charge="0.01888" shct="0.72" />
<GeneralizedKirkwood type="127" charge="0.27710" shct="0.72" /> <GeneralizedKirkwood type="115" charge="0.06585" shct="0.85" />
<GeneralizedKirkwood type="128" charge="0.07110" shct="0.85" /> <GeneralizedKirkwood type="116" charge="0.36202" shct="0.72" />
<GeneralizedKirkwood type="129" charge="-0.48774" shct="0.79" /> <GeneralizedKirkwood type="117" charge="0.08951" shct="0.85" />
<GeneralizedKirkwood type="130" charge="-0.07191" shct="0.72" /> <GeneralizedKirkwood type="118" charge="-0.07427" shct="0.79" />
<GeneralizedKirkwood type="131" charge="0.09317" shct="0.85" /> <GeneralizedKirkwood type="119" charge="0.13793" shct="0.85" />
<GeneralizedKirkwood type="132" charge="0.21765" shct="0.72" /> <GeneralizedKirkwood type="120" charge="-0.07944" shct="0.72" />
<GeneralizedKirkwood type="133" charge="-0.58085" shct="0.79" /> <GeneralizedKirkwood type="121" charge="0.08230" shct="0.85" />
<GeneralizedKirkwood type="134" charge="-0.05319" shct="0.72" /> <GeneralizedKirkwood type="122" charge="0.02915" shct="0.72" />
<GeneralizedKirkwood type="135" charge="0.03309" shct="0.85" /> <GeneralizedKirkwood type="123" charge="-0.20791" shct="0.79" />
<GeneralizedKirkwood type="136" charge="0.31901" shct="0.72" /> <GeneralizedKirkwood type="124" charge="0.22642" shct="0.85" />
<GeneralizedKirkwood type="137" charge="0.03395" shct="0.85" /> <GeneralizedKirkwood type="125" charge="0.02645" shct="0.72" />
<GeneralizedKirkwood type="138" charge="-0.11867" shct="0.79" /> <GeneralizedKirkwood type="126" charge="0.05039" shct="0.85" />
<GeneralizedKirkwood type="139" charge="0.10470" shct="0.85" /> <GeneralizedKirkwood type="127" charge="0.27710" shct="0.72" />
<GeneralizedKirkwood type="140" charge="-0.33040" shct="0.72" /> <GeneralizedKirkwood type="128" charge="0.07110" shct="0.85" />
<GeneralizedKirkwood type="141" charge="0.04893" shct="0.85" /> <GeneralizedKirkwood type="129" charge="-0.48774" shct="0.79" />
<GeneralizedKirkwood type="142" charge="1.01644" shct="0.72" /> <GeneralizedKirkwood type="130" charge="-0.07191" shct="0.72" />
<GeneralizedKirkwood type="143" charge="-0.85689" shct="0.85" /> <GeneralizedKirkwood type="131" charge="0.09317" shct="0.85" />
<GeneralizedKirkwood type="144" charge="-0.09907" shct="0.72" /> <GeneralizedKirkwood type="132" charge="0.21765" shct="0.72" />
<GeneralizedKirkwood type="144" charge="-0.20674" shct="0.72" /> <GeneralizedKirkwood type="133" charge="-0.58085" shct="0.79" />
<GeneralizedKirkwood type="145" charge="0.09104" shct="0.85" /> <GeneralizedKirkwood type="134" charge="-0.05319" shct="0.72" />
<GeneralizedKirkwood type="146" charge="0.80267" shct="0.72" /> <GeneralizedKirkwood type="135" charge="0.03309" shct="0.85" />
<GeneralizedKirkwood type="147" charge="-0.61184" shct="0.85" /> <GeneralizedKirkwood type="136" charge="0.31901" shct="0.72" />
<GeneralizedKirkwood type="148" charge="-0.44451" shct="0.85" /> <GeneralizedKirkwood type="137" charge="0.03395" shct="0.85" />
<GeneralizedKirkwood type="149" charge="0.24079" shct="0.85" /> <GeneralizedKirkwood type="138" charge="-0.11867" shct="0.79" />
<GeneralizedKirkwood type="150" charge="-0.15072" shct="0.72" /> <GeneralizedKirkwood type="139" charge="0.10470" shct="0.85" />
<GeneralizedKirkwood type="150" charge="-0.14858" shct="0.72" /> <GeneralizedKirkwood type="140" charge="-0.33040" shct="0.72" />
<GeneralizedKirkwood type="151" charge="0.09679" shct="0.85" /> <GeneralizedKirkwood type="141" charge="0.04893" shct="0.85" />
<GeneralizedKirkwood type="152" charge="0.76960" shct="0.72" /> <GeneralizedKirkwood type="142" charge="1.01644" shct="0.72" />
<GeneralizedKirkwood type="153" charge="-0.72950" shct="0.85" /> <GeneralizedKirkwood type="143" charge="-0.85689" shct="0.85" />
<GeneralizedKirkwood type="154" charge="-0.38020" shct="0.79" /> <GeneralizedKirkwood type="144" charge="-0.09907" shct="0.72" />
<GeneralizedKirkwood type="155" charge="0.18368" shct="0.85" /> <GeneralizedKirkwood type="145" charge="0.09104" shct="0.85" />
<GeneralizedKirkwood type="156" charge="0.00410" shct="0.72" /> <GeneralizedKirkwood type="146" charge="0.80267" shct="0.72" />
<GeneralizedKirkwood type="157" charge="0.04082" shct="0.85" /> <GeneralizedKirkwood type="147" charge="-0.61184" shct="0.85" />
<GeneralizedKirkwood type="158" charge="-0.36014" shct="0.72" /> <GeneralizedKirkwood type="148" charge="-0.44451" shct="0.85" />
<GeneralizedKirkwood type="159" charge="-0.00356" shct="0.85" /> <GeneralizedKirkwood type="149" charge="0.24079" shct="0.85" />
<GeneralizedKirkwood type="160" charge="1.14596" shct="0.72" /> <GeneralizedKirkwood type="150" charge="-0.15072" shct="0.72" />
<GeneralizedKirkwood type="161" charge="-0.89716" shct="0.85" /> <GeneralizedKirkwood type="151" charge="0.09679" shct="0.85" />
<GeneralizedKirkwood type="162" charge="-0.07714" shct="0.72" /> <GeneralizedKirkwood type="152" charge="0.76960" shct="0.72" />
<GeneralizedKirkwood type="163" charge="0.09378" shct="0.85" /> <GeneralizedKirkwood type="153" charge="-0.72950" shct="0.85" />
<GeneralizedKirkwood type="164" charge="-0.12108" shct="0.72" /> <GeneralizedKirkwood type="154" charge="-0.38020" shct="0.79" />
<GeneralizedKirkwood type="165" charge="0.05947" shct="0.85" /> <GeneralizedKirkwood type="155" charge="0.18368" shct="0.85" />
<GeneralizedKirkwood type="166" charge="-0.02949" shct="0.72" /> <GeneralizedKirkwood type="156" charge="0.00410" shct="0.72" />
<GeneralizedKirkwood type="167" charge="0.06373" shct="0.85" /> <GeneralizedKirkwood type="157" charge="0.04082" shct="0.85" />
<GeneralizedKirkwood type="168" charge="-0.07285" shct="0.72" /> <GeneralizedKirkwood type="158" charge="-0.36014" shct="0.72" />
<GeneralizedKirkwood type="169" charge="0.00251" shct="0.85" /> <GeneralizedKirkwood type="159" charge="-0.00356" shct="0.85" />
<GeneralizedKirkwood type="170" charge="0.06969" shct="0.96" /> <GeneralizedKirkwood type="160" charge="1.14596" shct="0.72" />
<GeneralizedKirkwood type="171" charge="-0.15553" shct="0.72" /> <GeneralizedKirkwood type="161" charge="-0.89716" shct="0.85" />
<GeneralizedKirkwood type="172" charge="0.04194" shct="0.85" /> <GeneralizedKirkwood type="162" charge="-0.07714" shct="0.72" />
<GeneralizedKirkwood type="173" charge="0.01417" shct="0.72" /> <GeneralizedKirkwood type="163" charge="0.09378" shct="0.85" />
<GeneralizedKirkwood type="174" charge="0.06168" shct="0.85" /> <GeneralizedKirkwood type="164" charge="-0.20674" shct="0.72" />
<GeneralizedKirkwood type="175" charge="-0.23796" shct="0.72" /> <GeneralizedKirkwood type="165" charge="0.09104" shct="0.85" />
<GeneralizedKirkwood type="175" charge="-0.14658" shct="0.72" /> <GeneralizedKirkwood type="166" charge="0.80267" shct="0.72" />
<GeneralizedKirkwood type="176" charge="0.07914" shct="0.85" /> <GeneralizedKirkwood type="167" charge="-0.61184" shct="0.85" />
<GeneralizedKirkwood type="177" charge="-0.12517" shct="0.72" /> <GeneralizedKirkwood type="168" charge="-0.44451" shct="0.85" />
<GeneralizedKirkwood type="178" charge="0.07947" shct="0.85" /> <GeneralizedKirkwood type="169" charge="0.24079" shct="0.85" />
<GeneralizedKirkwood type="179" charge="-0.00637" shct="0.72" /> <GeneralizedKirkwood type="170" charge="-0.12108" shct="0.72" />
<GeneralizedKirkwood type="180" charge="0.10424" shct="0.85" /> <GeneralizedKirkwood type="171" charge="0.05947" shct="0.85" />
<GeneralizedKirkwood type="181" charge="0.10679" shct="0.79" /> <GeneralizedKirkwood type="172" charge="-0.14858" shct="0.72" />
<GeneralizedKirkwood type="182" charge="0.19274" shct="0.85" /> <GeneralizedKirkwood type="173" charge="0.09679" shct="0.85" />
<GeneralizedKirkwood type="183" charge="-0.11624" shct="0.72" /> <GeneralizedKirkwood type="174" charge="0.76960" shct="0.72" />
<GeneralizedKirkwood type="184" charge="0.05672" shct="0.85" /> <GeneralizedKirkwood type="175" charge="-0.72950" shct="0.85" />
<GeneralizedKirkwood type="185" charge="0.11242" shct="0.72" /> <GeneralizedKirkwood type="176" charge="-0.38020" shct="0.79" />
<GeneralizedKirkwood type="186" charge="0.02390" shct="0.85" /> <GeneralizedKirkwood type="177" charge="0.18368" shct="0.85" />
<GeneralizedKirkwood type="187" charge="-0.30941" shct="0.79" /> <GeneralizedKirkwood type="178" charge="-0.02949" shct="0.72" />
<GeneralizedKirkwood type="188" charge="0.08213" shct="0.85" /> <GeneralizedKirkwood type="179" charge="0.06373" shct="0.85" />
<GeneralizedKirkwood type="189" charge="-0.05810" shct="0.72" /> <GeneralizedKirkwood type="180" charge="-0.07285" shct="0.72" />
<GeneralizedKirkwood type="190" charge="0.07332" shct="0.85" /> <GeneralizedKirkwood type="181" charge="0.00251" shct="0.85" />
<GeneralizedKirkwood type="191" charge="-0.12460" shct="0.72" /> <GeneralizedKirkwood type="182" charge="0.06969" shct="0.96" />
<GeneralizedKirkwood type="192" charge="0.10013" shct="0.85" /> <GeneralizedKirkwood type="183" charge="-0.15553" shct="0.72" />
<GeneralizedKirkwood type="193" charge="-0.00504" shct="0.72" /> <GeneralizedKirkwood type="184" charge="0.04194" shct="0.85" />
<GeneralizedKirkwood type="194" charge="0.06386" shct="0.85" /> <GeneralizedKirkwood type="185" charge="0.01417" shct="0.72" />
<GeneralizedKirkwood type="195" charge="-0.26789" shct="0.79" /> <GeneralizedKirkwood type="186" charge="0.06168" shct="0.85" />
<GeneralizedKirkwood type="196" charge="0.14895" shct="0.85" /> <GeneralizedKirkwood type="187" charge="-0.14658" shct="0.72" />
<GeneralizedKirkwood type="197" charge="0.90680" shct="0.72" /> <GeneralizedKirkwood type="188" charge="0.07914" shct="0.85" />
<GeneralizedKirkwood type="198" charge="-0.30169" shct="0.79" /> <GeneralizedKirkwood type="189" charge="-0.12517" shct="0.72" />
<GeneralizedKirkwood type="199" charge="0.14969" shct="0.85" /> <GeneralizedKirkwood type="190" charge="0.07947" shct="0.85" />
<GeneralizedKirkwood type="200" charge="0.01417" shct="0.72" /> <GeneralizedKirkwood type="191" charge="-0.00637" shct="0.72" />
<GeneralizedKirkwood type="201" charge="0.06168" shct="0.85" /> <GeneralizedKirkwood type="192" charge="0.10424" shct="0.85" />
<GeneralizedKirkwood type="202" charge="-0.12127" shct="0.72" /> <GeneralizedKirkwood type="193" charge="0.10679" shct="0.79" />
<GeneralizedKirkwood type="203" charge="0.08337" shct="0.85" /> <GeneralizedKirkwood type="194" charge="0.19274" shct="0.85" />
<GeneralizedKirkwood type="204" charge="-0.00637" shct="0.72" /> <GeneralizedKirkwood type="195" charge="0.01417" shct="0.72" />
<GeneralizedKirkwood type="205" charge="0.10424" shct="0.85" /> <GeneralizedKirkwood type="196" charge="0.06168" shct="0.85" />
<GeneralizedKirkwood type="206" charge="0.10679" shct="0.79" /> <GeneralizedKirkwood type="197" charge="-0.23796" shct="0.72" />
<GeneralizedKirkwood type="207" charge="0.19274" shct="0.85" /> <GeneralizedKirkwood type="198" charge="0.07914" shct="0.85" />
<GeneralizedKirkwood type="208" charge="-0.19495" shct="0.72" /> <GeneralizedKirkwood type="199" charge="-0.11624" shct="0.72" />
<GeneralizedKirkwood type="209" charge="0.07797" shct="0.85" /> <GeneralizedKirkwood type="200" charge="0.05672" shct="0.85" />
<GeneralizedKirkwood type="210" charge="0.70656" shct="0.72" /> <GeneralizedKirkwood type="201" charge="0.11242" shct="0.72" />
<GeneralizedKirkwood type="211" charge="-0.74615" shct="0.85" /> <GeneralizedKirkwood type="202" charge="0.02390" shct="0.85" />
<GeneralizedKirkwood type="212" charge="-0.25887" shct="0.79" /> <GeneralizedKirkwood type="203" charge="-0.30941" shct="0.79" />
<GeneralizedKirkwood type="213" charge="0.12975" shct="0.85" /> <GeneralizedKirkwood type="204" charge="0.08213" shct="0.85" />
<GeneralizedKirkwood type="214" charge="-0.27516" shct="0.79" /> <GeneralizedKirkwood type="205" charge="-0.05810" shct="0.72" />
<GeneralizedKirkwood type="215" charge="0.12524" shct="0.85" /> <GeneralizedKirkwood type="206" charge="0.07332" shct="0.85" />
<GeneralizedKirkwood type="216" charge="-0.00902" shct="0.72" /> <GeneralizedKirkwood type="207" charge="-0.12460" shct="0.72" />
<GeneralizedKirkwood type="217" charge="0.05319" shct="0.85" /> <GeneralizedKirkwood type="208" charge="0.10013" shct="0.85" />
<GeneralizedKirkwood type="218" charge="0.11164" shct="0.79" /> <GeneralizedKirkwood type="209" charge="-0.00504" shct="0.72" />
<GeneralizedKirkwood type="218" charge="0.11164" shct="0.79" /> <GeneralizedKirkwood type="210" charge="0.06386" shct="0.85" />
<GeneralizedKirkwood type="218" charge="0.11164" shct="0.79" /> <GeneralizedKirkwood type="211" charge="-0.26789" shct="0.79" />
<GeneralizedKirkwood type="218" charge="0.11164" shct="0.79" /> <GeneralizedKirkwood type="212" charge="0.14895" shct="0.85" />
<GeneralizedKirkwood type="219" charge="0.21240" shct="0.85" /> <GeneralizedKirkwood type="213" charge="0.90680" shct="0.72" />
<GeneralizedKirkwood type="219" charge="0.21240" shct="0.85" /> <GeneralizedKirkwood type="214" charge="-0.30169" shct="0.79" />
<GeneralizedKirkwood type="219" charge="0.21240" shct="0.85" /> <GeneralizedKirkwood type="215" charge="0.14969" shct="0.85" />
<GeneralizedKirkwood type="219" charge="0.21240" shct="0.85" /> <GeneralizedKirkwood type="216" charge="0.01417" shct="0.72" />
<GeneralizedKirkwood type="220" charge="1.02669" shct="0.72" /> <GeneralizedKirkwood type="217" charge="0.06168" shct="0.85" />
<GeneralizedKirkwood type="221" charge="-0.90443" shct="0.85" /> <GeneralizedKirkwood type="218" charge="-0.12127" shct="0.72" />
<GeneralizedKirkwood type="222" charge="0.07219" shct="0.79" /> <GeneralizedKirkwood type="219" charge="0.08337" shct="0.85" />
<GeneralizedKirkwood type="223" charge="0.23262" shct="0.85" /> <GeneralizedKirkwood type="220" charge="-0.00637" shct="0.72" />
<GeneralizedKirkwood type="224" charge="-0.16428" shct="0.72" /> <GeneralizedKirkwood type="221" charge="0.10424" shct="0.85" />
<GeneralizedKirkwood type="225" charge="0.88092" shct="0.72" /> <GeneralizedKirkwood type="222" charge="0.10679" shct="0.79" />
<GeneralizedKirkwood type="226" charge="-0.74794" shct="0.85" /> <GeneralizedKirkwood type="223" charge="0.19274" shct="0.85" />
<GeneralizedKirkwood type="227" charge="0.12611" shct="0.85" /> <GeneralizedKirkwood type="224" charge="-0.19495" shct="0.72" />
<GeneralizedKirkwood type="228" charge="-0.04567" shct="0.72" /> <GeneralizedKirkwood type="225" charge="0.07797" shct="0.85" />
<GeneralizedKirkwood type="229" charge="0.10559" shct="0.85" /> <GeneralizedKirkwood type="226" charge="0.70656" shct="0.72" />
<GeneralizedKirkwood type="230" charge="-0.12218" shct="0.79" /> <GeneralizedKirkwood type="227" charge="-0.74615" shct="0.85" />
<GeneralizedKirkwood type="231" charge="0.10618" shct="0.72" /> <GeneralizedKirkwood type="228" charge="-0.25887" shct="0.79" />
<GeneralizedKirkwood type="232" charge="0.03294" shct="0.72" /> <GeneralizedKirkwood type="229" charge="0.12975" shct="0.85" />
<GeneralizedKirkwood type="233" charge="-0.29610" shct="0.79" /> <GeneralizedKirkwood type="230" charge="-0.27516" shct="0.79" />
<GeneralizedKirkwood type="234" charge="0.12091" shct="0.72" /> <GeneralizedKirkwood type="231" charge="0.12524" shct="0.85" />
<GeneralizedKirkwood type="235" charge="-0.28556" shct="0.79" /> <GeneralizedKirkwood type="232" charge="-0.00902" shct="0.72" />
<GeneralizedKirkwood type="236" charge="0.09440" shct="0.72" /> <GeneralizedKirkwood type="233" charge="0.05319" shct="0.85" />
<GeneralizedKirkwood type="237" charge="-0.30504" shct="0.79" /> <GeneralizedKirkwood type="234" charge="0.11164" shct="0.79" />
<GeneralizedKirkwood type="238" charge="0.11701" shct="0.72" /> <GeneralizedKirkwood type="234" charge="0.11164" shct="0.79" />
<GeneralizedKirkwood type="239" charge="0.10987" shct="0.85" /> <GeneralizedKirkwood type="234" charge="0.11164" shct="0.79" />
<GeneralizedKirkwood type="240" charge="-0.28195" shct="0.79" /> <GeneralizedKirkwood type="234" charge="0.11164" shct="0.79" />
<GeneralizedKirkwood type="241" charge="0.23408" shct="0.85" /> <GeneralizedKirkwood type="235" charge="0.21240" shct="0.85" />
<GeneralizedKirkwood type="242" charge="0.23408" shct="0.85" /> <GeneralizedKirkwood type="235" charge="0.21240" shct="0.85" />
<GeneralizedKirkwood type="243" charge="0.12346" shct="0.85" /> <GeneralizedKirkwood type="235" charge="0.21240" shct="0.85" />
<GeneralizedKirkwood type="244" charge="-0.12896" shct="0.79" /> <GeneralizedKirkwood type="235" charge="0.21240" shct="0.85" />
<GeneralizedKirkwood type="245" charge="0.25555" shct="0.72" /> <GeneralizedKirkwood type="236" charge="-0.29203" shct="0.79" />
<GeneralizedKirkwood type="246" charge="-0.29612" shct="0.79" /> <GeneralizedKirkwood type="236" charge="-0.29203" shct="0.79" />
<GeneralizedKirkwood type="247" charge="0.10206" shct="0.72" /> <GeneralizedKirkwood type="236" charge="-0.29203" shct="0.79" />
<GeneralizedKirkwood type="248" charge="-0.08445" shct="0.72" /> <GeneralizedKirkwood type="236" charge="-0.29203" shct="0.79" />
<GeneralizedKirkwood type="249" charge="0.09191" shct="0.72" /> <GeneralizedKirkwood type="237" charge="0.09729" shct="0.85" />
<GeneralizedKirkwood type="250" charge="-0.42963" shct="0.85" /> <GeneralizedKirkwood type="238" charge="1.02669" shct="0.72" />
<GeneralizedKirkwood type="251" charge="-0.28291" shct="0.79" /> <GeneralizedKirkwood type="239" charge="-0.90443" shct="0.85" />
<GeneralizedKirkwood type="252" charge="0.22172" shct="0.85" /> <GeneralizedKirkwood type="240" charge="0.90327" shct="0.72" />
<GeneralizedKirkwood type="253" charge="0.22172" shct="0.85" /> <GeneralizedKirkwood type="240" charge="0.90327" shct="0.72" />
<GeneralizedKirkwood type="254" charge="0.09969" shct="0.85" /> <GeneralizedKirkwood type="240" charge="0.90327" shct="0.72" />
<GeneralizedKirkwood type="255" charge="0.11152" shct="0.85" /> <GeneralizedKirkwood type="240" charge="0.90327" shct="0.72" />
<GeneralizedKirkwood type="256" charge="-0.12123" shct="0.79" /> <GeneralizedKirkwood type="241" charge="-0.65062" shct="0.85" />
<GeneralizedKirkwood type="257" charge="0.11988" shct="0.72" /> <GeneralizedKirkwood type="241" charge="-0.65062" shct="0.85" />
<GeneralizedKirkwood type="258" charge="0.05939" shct="0.72" /> <GeneralizedKirkwood type="241" charge="-0.65062" shct="0.85" />
<GeneralizedKirkwood type="259" charge="-0.25427" shct="0.79" /> <GeneralizedKirkwood type="241" charge="-0.65062" shct="0.85" />
<GeneralizedKirkwood type="260" charge="0.05900" shct="0.72" /> <GeneralizedKirkwood type="242" charge="-0.47859" shct="0.85" />
<GeneralizedKirkwood type="261" charge="-0.32183" shct="0.79" /> <GeneralizedKirkwood type="243" charge="0.24567" shct="0.85" />
<GeneralizedKirkwood type="262" charge="0.16650" shct="0.72" /> <GeneralizedKirkwood type="244" charge="0.07219" shct="0.79" />
<GeneralizedKirkwood type="263" charge="-0.20681" shct="0.79" /> <GeneralizedKirkwood type="245" charge="0.23262" shct="0.85" />
<GeneralizedKirkwood type="264" charge="0.22596" shct="0.72" /> <GeneralizedKirkwood type="246" charge="-0.16428" shct="0.72" />
<GeneralizedKirkwood type="265" charge="0.25827" shct="0.85" /> <GeneralizedKirkwood type="247" charge="0.93900" shct="0.72" />
<GeneralizedKirkwood type="266" charge="-0.30237" shct="0.79" /> <GeneralizedKirkwood type="248" charge="-0.74794" shct="0.85" />
<GeneralizedKirkwood type="267" charge="0.22815" shct="0.85" /> <GeneralizedKirkwood type="249" charge="0.12611" shct="0.85" />
<GeneralizedKirkwood type="268" charge="0.22815" shct="0.85" /> <GeneralizedKirkwood type="250" charge="-0.04567" shct="0.72" />
<GeneralizedKirkwood type="269" charge="-0.37776" shct="0.85" /> <GeneralizedKirkwood type="251" charge="0.10559" shct="0.85" />
<GeneralizedKirkwood type="270" charge="0.12107" shct="0.85" /> <GeneralizedKirkwood type="252" charge="-0.12218" shct="0.79" />
<GeneralizedKirkwood type="271" charge="-0.15031" shct="0.79" /> <GeneralizedKirkwood type="253" charge="0.10618" shct="0.72" />
<GeneralizedKirkwood type="272" charge="0.25814" shct="0.72" /> <GeneralizedKirkwood type="254" charge="0.03294" shct="0.72" />
<GeneralizedKirkwood type="273" charge="-0.18494" shct="0.79" /> <GeneralizedKirkwood type="255" charge="-0.29610" shct="0.79" />
<GeneralizedKirkwood type="274" charge="0.20468" shct="0.72" /> <GeneralizedKirkwood type="256" charge="0.12091" shct="0.72" />
<GeneralizedKirkwood type="275" charge="-0.10776" shct="0.72" /> <GeneralizedKirkwood type="257" charge="-0.28556" shct="0.79" />
<GeneralizedKirkwood type="276" charge="0.02014" shct="0.72" /> <GeneralizedKirkwood type="258" charge="0.09440" shct="0.72" />
<GeneralizedKirkwood type="277" charge="-0.42656" shct="0.85" /> <GeneralizedKirkwood type="259" charge="-0.30504" shct="0.79" />
<GeneralizedKirkwood type="278" charge="0.27344" shct="0.85" /> <GeneralizedKirkwood type="260" charge="0.11701" shct="0.72" />
<GeneralizedKirkwood type="279" charge="-0.40427" shct="0.85" /> <GeneralizedKirkwood type="261" charge="0.10987" shct="0.85" />
<GeneralizedKirkwood type="280" charge="-0.09928" shct="0.72" /> <GeneralizedKirkwood type="262" charge="-0.28195" shct="0.79" />
<GeneralizedKirkwood type="281" charge="0.12786" shct="0.85" /> <GeneralizedKirkwood type="263" charge="0.23408" shct="0.85" />
<GeneralizedKirkwood type="282" charge="0.11524" shct="0.85" /> <GeneralizedKirkwood type="264" charge="0.23408" shct="0.85" />
<GeneralizedKirkwood type="283" charge="-0.11970" shct="0.79" /> <GeneralizedKirkwood type="265" charge="0.12346" shct="0.85" />
<GeneralizedKirkwood type="284" charge="0.26026" shct="0.72" /> <GeneralizedKirkwood type="266" charge="-0.12896" shct="0.79" />
<GeneralizedKirkwood type="285" charge="-0.18804" shct="0.79" /> <GeneralizedKirkwood type="267" charge="0.25555" shct="0.72" />
<GeneralizedKirkwood type="286" charge="0.20160" shct="0.72" /> <GeneralizedKirkwood type="268" charge="-0.29612" shct="0.79" />
<GeneralizedKirkwood type="287" charge="-0.05028" shct="0.72" /> <GeneralizedKirkwood type="269" charge="0.10206" shct="0.72" />
<GeneralizedKirkwood type="288" charge="0.07568" shct="0.72" /> <GeneralizedKirkwood type="270" charge="-0.08445" shct="0.72" />
<GeneralizedKirkwood type="289" charge="-0.42057" shct="0.85" /> <GeneralizedKirkwood type="271" charge="0.09191" shct="0.72" />
<GeneralizedKirkwood type="290" charge="0.27376" shct="0.85" /> <GeneralizedKirkwood type="272" charge="-0.42963" shct="0.85" />
<GeneralizedKirkwood type="291" charge="-0.38720" shct="0.85" /> <GeneralizedKirkwood type="273" charge="-0.28291" shct="0.79" />
<GeneralizedKirkwood type="292" charge="0.12060" shct="0.85" /> <GeneralizedKirkwood type="274" charge="0.22172" shct="0.85" />
<GeneralizedKirkwood type="293" charge="0.11599" shct="0.85" /> <GeneralizedKirkwood type="275" charge="0.22172" shct="0.85" />
<GeneralizedKirkwood type="294" charge="-0.52467" shct="0.85" /> <GeneralizedKirkwood type="276" charge="0.09969" shct="0.85" />
<GeneralizedKirkwood type="295" charge="0.05049" shct="0.72" /> <GeneralizedKirkwood type="277" charge="0.11152" shct="0.85" />
<GeneralizedKirkwood type="296" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="278" charge="-0.12123" shct="0.79" />
<GeneralizedKirkwood type="297" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="279" charge="0.11988" shct="0.72" />
<GeneralizedKirkwood type="298" charge="0.10423" shct="0.72" /> <GeneralizedKirkwood type="280" charge="0.05939" shct="0.72" />
<GeneralizedKirkwood type="299" charge="0.13028" shct="0.85" /> <GeneralizedKirkwood type="281" charge="-0.25427" shct="0.79" />
<GeneralizedKirkwood type="300" charge="-0.40197" shct="0.85" /> <GeneralizedKirkwood type="282" charge="0.05900" shct="0.72" />
<GeneralizedKirkwood type="301" charge="0.06316" shct="0.72" /> <GeneralizedKirkwood type="283" charge="-0.32183" shct="0.79" />
<GeneralizedKirkwood type="302" charge="0.18443" shct="0.85" /> <GeneralizedKirkwood type="284" charge="0.16650" shct="0.72" />
<GeneralizedKirkwood type="303" charge="0.10143" shct="0.72" /> <GeneralizedKirkwood type="285" charge="-0.20681" shct="0.79" />
<GeneralizedKirkwood type="304" charge="0.11227" shct="0.85" /> <GeneralizedKirkwood type="286" charge="0.22596" shct="0.72" />
<GeneralizedKirkwood type="305" charge="0.06213" shct="0.72" /> <GeneralizedKirkwood type="287" charge="0.25827" shct="0.85" />
<GeneralizedKirkwood type="306" charge="0.11711" shct="0.85" /> <GeneralizedKirkwood type="288" charge="-0.30237" shct="0.79" />
<GeneralizedKirkwood type="307" charge="-0.47891" shct="0.85" /> <GeneralizedKirkwood type="289" charge="0.22815" shct="0.85" />
<GeneralizedKirkwood type="308" charge="0.32469" shct="0.85" /> <GeneralizedKirkwood type="290" charge="0.22815" shct="0.85" />
<GeneralizedKirkwood type="309" charge="-0.53467" shct="0.85" /> <GeneralizedKirkwood type="291" charge="-0.37776" shct="0.85" />
<GeneralizedKirkwood type="310" charge="-0.52467" shct="0.85" /> <GeneralizedKirkwood type="292" charge="0.12107" shct="0.85" />
<GeneralizedKirkwood type="311" charge="0.05049" shct="0.72" /> <GeneralizedKirkwood type="293" charge="-0.15031" shct="0.79" />
<GeneralizedKirkwood type="312" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="294" charge="0.25814" shct="0.72" />
<GeneralizedKirkwood type="313" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="295" charge="-0.18494" shct="0.79" />
<GeneralizedKirkwood type="314" charge="0.10423" shct="0.72" /> <GeneralizedKirkwood type="296" charge="0.20468" shct="0.72" />
<GeneralizedKirkwood type="315" charge="0.13028" shct="0.85" /> <GeneralizedKirkwood type="297" charge="-0.10776" shct="0.72" />
<GeneralizedKirkwood type="316" charge="-0.40197" shct="0.85" /> <GeneralizedKirkwood type="298" charge="0.02014" shct="0.72" />
<GeneralizedKirkwood type="317" charge="0.06316" shct="0.72" /> <GeneralizedKirkwood type="299" charge="-0.42656" shct="0.85" />
<GeneralizedKirkwood type="318" charge="0.18443" shct="0.85" /> <GeneralizedKirkwood type="300" charge="0.27344" shct="0.85" />
<GeneralizedKirkwood type="319" charge="0.10143" shct="0.72" /> <GeneralizedKirkwood type="301" charge="-0.40427" shct="0.85" />
<GeneralizedKirkwood type="320" charge="0.11227" shct="0.85" /> <GeneralizedKirkwood type="302" charge="-0.09928" shct="0.72" />
<GeneralizedKirkwood type="321" charge="0.06213" shct="0.72" /> <GeneralizedKirkwood type="303" charge="0.12786" shct="0.85" />
<GeneralizedKirkwood type="322" charge="0.11711" shct="0.85" /> <GeneralizedKirkwood type="304" charge="0.11524" shct="0.85" />
<GeneralizedKirkwood type="323" charge="-0.47891" shct="0.85" /> <GeneralizedKirkwood type="305" charge="-0.11970" shct="0.79" />
<GeneralizedKirkwood type="324" charge="0.32469" shct="0.85" /> <GeneralizedKirkwood type="306" charge="0.26026" shct="0.72" />
<GeneralizedKirkwood type="325" charge="-0.53467" shct="0.85" /> <GeneralizedKirkwood type="307" charge="-0.18804" shct="0.79" />
<GeneralizedKirkwood type="326" charge="-0.52467" shct="0.85" /> <GeneralizedKirkwood type="308" charge="0.20160" shct="0.72" />
<GeneralizedKirkwood type="327" charge="0.00960" shct="0.72" /> <GeneralizedKirkwood type="309" charge="-0.05028" shct="0.72" />
<GeneralizedKirkwood type="328" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="310" charge="0.07568" shct="0.72" />
<GeneralizedKirkwood type="329" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="311" charge="-0.42057" shct="0.85" />
<GeneralizedKirkwood type="330" charge="0.15826" shct="0.72" /> <GeneralizedKirkwood type="312" charge="0.27376" shct="0.85" />
<GeneralizedKirkwood type="331" charge="0.12800" shct="0.85" /> <GeneralizedKirkwood type="313" charge="-0.38720" shct="0.85" />
<GeneralizedKirkwood type="332" charge="-0.38842" shct="0.85" /> <GeneralizedKirkwood type="314" charge="0.12060" shct="0.85" />
<GeneralizedKirkwood type="333" charge="0.06720" shct="0.72" /> <GeneralizedKirkwood type="315" charge="0.11599" shct="0.85" />
<GeneralizedKirkwood type="334" charge="0.12287" shct="0.85" /> <GeneralizedKirkwood type="316" charge="-0.52467" shct="0.85" />
<GeneralizedKirkwood type="335" charge="0.07060" shct="0.72" /> <GeneralizedKirkwood type="317" charge="0.05049" shct="0.72" />
<GeneralizedKirkwood type="336" charge="0.10297" shct="0.85" /> <GeneralizedKirkwood type="318" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="337" charge="-0.10232" shct="0.72" /> <GeneralizedKirkwood type="319" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="338" charge="0.10225" shct="0.85" /> <GeneralizedKirkwood type="320" charge="0.10423" shct="0.72" />
<GeneralizedKirkwood type="339" charge="0.09833" shct="0.85" /> <GeneralizedKirkwood type="321" charge="0.13028" shct="0.85" />
<GeneralizedKirkwood type="340" charge="-0.53467" shct="0.85" /> <GeneralizedKirkwood type="322" charge="-0.40197" shct="0.85" />
<GeneralizedKirkwood type="341" charge="-0.52467" shct="0.85" /> <GeneralizedKirkwood type="323" charge="0.06316" shct="0.72" />
<GeneralizedKirkwood type="342" charge="0.00960" shct="0.72" /> <GeneralizedKirkwood type="324" charge="0.18443" shct="0.85" />
<GeneralizedKirkwood type="343" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="325" charge="0.10143" shct="0.72" />
<GeneralizedKirkwood type="344" charge="0.07556" shct="0.85" /> <GeneralizedKirkwood type="326" charge="0.11227" shct="0.85" />
<GeneralizedKirkwood type="345" charge="0.15826" shct="0.72" /> <GeneralizedKirkwood type="327" charge="0.06213" shct="0.72" />
<GeneralizedKirkwood type="346" charge="0.12800" shct="0.85" /> <GeneralizedKirkwood type="328" charge="0.11711" shct="0.85" />
<GeneralizedKirkwood type="347" charge="-0.38842" shct="0.85" /> <GeneralizedKirkwood type="329" charge="-0.47891" shct="0.85" />
<GeneralizedKirkwood type="348" charge="0.06720" shct="0.72" /> <GeneralizedKirkwood type="330" charge="0.32469" shct="0.85" />
<GeneralizedKirkwood type="349" charge="0.12287" shct="0.85" /> <GeneralizedKirkwood type="331" charge="-0.53467" shct="0.85" />
<GeneralizedKirkwood type="350" charge="0.07060" shct="0.72" /> <GeneralizedKirkwood type="332" charge="-0.52467" shct="0.85" />
<GeneralizedKirkwood type="351" charge="0.10297" shct="0.85" /> <GeneralizedKirkwood type="333" charge="0.05049" shct="0.72" />
<GeneralizedKirkwood type="352" charge="-0.10232" shct="0.72" /> <GeneralizedKirkwood type="334" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="353" charge="0.10225" shct="0.85" /> <GeneralizedKirkwood type="335" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="354" charge="0.09833" shct="0.85" /> <GeneralizedKirkwood type="336" charge="0.10423" shct="0.72" />
<GeneralizedKirkwood type="355" charge="-0.53467" shct="0.85" /> <GeneralizedKirkwood type="337" charge="0.13028" shct="0.85" />
<GeneralizedKirkwood type="356" charge="0.90070" shct="0.86" /> <GeneralizedKirkwood type="338" charge="-0.40197" shct="0.85" />
<GeneralizedKirkwood type="357" charge="-0.62196" shct="0.85" /> <GeneralizedKirkwood type="339" charge="0.06316" shct="0.72" />
<GeneralizedKirkwood type="358" charge="-0.53491" shct="0.85" /> <GeneralizedKirkwood type="340" charge="0.18443" shct="0.85" />
<GeneralizedKirkwood type="358" charge="-0.53491" shct="0.85" /> <GeneralizedKirkwood type="341" charge="0.10143" shct="0.72" />
<GeneralizedKirkwood type="359" charge="0.34636" shct="0.85" /> <GeneralizedKirkwood type="342" charge="0.11227" shct="0.85" />
<GeneralizedKirkwood type="359" charge="0.34636" shct="0.85" /> <GeneralizedKirkwood type="343" charge="0.06213" shct="0.72" />
<GeneralizedKirkwood type="359" charge="0.34636" shct="0.85" /> <GeneralizedKirkwood type="344" charge="0.11711" shct="0.85" />
<GeneralizedKirkwood type="360" charge="-0.58166" shct="0.85" /> <GeneralizedKirkwood type="345" charge="-0.47891" shct="0.85" />
<GeneralizedKirkwood type="360" charge="-0.58166" shct="0.85" /> <GeneralizedKirkwood type="346" charge="0.32469" shct="0.85" />
<GeneralizedKirkwood type="361" charge="1.02369" shct="0.86" /> <GeneralizedKirkwood type="347" charge="-0.53467" shct="0.85" />
<GeneralizedKirkwood type="362" charge="-0.87686" shct="0.85" /> <GeneralizedKirkwood type="348" charge="-0.52467" shct="0.85" />
<GeneralizedKirkwood type="363" charge="-0.50819" shct="0.85" /> <GeneralizedKirkwood type="349" charge="0.00960" shct="0.72" />
<GeneralizedKirkwood type="363" charge="-0.50819" shct="0.85" /> <GeneralizedKirkwood type="350" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="364" charge="0.29418" shct="0.85" /> <GeneralizedKirkwood type="351" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="364" charge="0.29418" shct="0.85" /> <GeneralizedKirkwood type="352" charge="0.15826" shct="0.72" />
<GeneralizedKirkwood type="365" charge="-0.60712" shct="0.85" /> <GeneralizedKirkwood type="353" charge="0.12800" shct="0.85" />
<GeneralizedKirkwood type="365" charge="-0.60712" shct="0.85" /> <GeneralizedKirkwood type="354" charge="-0.38842" shct="0.85" />
<GeneralizedKirkwood type="366" charge="1.02369" shct="0.86" /> <GeneralizedKirkwood type="355" charge="0.06720" shct="0.72" />
<GeneralizedKirkwood type="367" charge="-0.87686" shct="0.85" /> <GeneralizedKirkwood type="356" charge="0.12287" shct="0.85" />
<GeneralizedKirkwood type="368" charge="0.90070" shct="0.86" /> <GeneralizedKirkwood type="357" charge="0.07060" shct="0.72" />
<GeneralizedKirkwood type="369" charge="-0.62196" shct="0.85" /> <GeneralizedKirkwood type="358" charge="0.10297" shct="0.85" />
<GeneralizedKirkwood type="370" charge="-0.53491" shct="0.85" /> <GeneralizedKirkwood type="359" charge="-0.10232" shct="0.72" />
<GeneralizedKirkwood type="370" charge="-0.53491" shct="0.85" /> <GeneralizedKirkwood type="360" charge="0.10225" shct="0.85" />
<GeneralizedKirkwood type="371" charge="0.34636" shct="0.85" /> <GeneralizedKirkwood type="361" charge="0.09833" shct="0.85" />
<GeneralizedKirkwood type="371" charge="0.34636" shct="0.85" /> <GeneralizedKirkwood type="362" charge="-0.53467" shct="0.85" />
<GeneralizedKirkwood type="372" charge="-0.58166" shct="0.85" /> <GeneralizedKirkwood type="363" charge="-0.52467" shct="0.85" />
<GeneralizedKirkwood type="372" charge="-0.58166" shct="0.85" /> <GeneralizedKirkwood type="364" charge="0.00960" shct="0.72" />
<GeneralizedKirkwood type="373" charge="1.02369" shct="0.86" /> <GeneralizedKirkwood type="365" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="374" charge="-0.87686" shct="0.85" /> <GeneralizedKirkwood type="366" charge="0.07556" shct="0.85" />
<GeneralizedKirkwood type="375" charge="-0.50819" shct="0.85" /> <GeneralizedKirkwood type="367" charge="0.15826" shct="0.72" />
<GeneralizedKirkwood type="375" charge="-0.50819" shct="0.85" /> <GeneralizedKirkwood type="368" charge="0.12800" shct="0.85" />
<GeneralizedKirkwood type="376" charge="0.29418" shct="0.85" /> <GeneralizedKirkwood type="369" charge="-0.38842" shct="0.85" />
<GeneralizedKirkwood type="376" charge="0.29418" shct="0.85" /> <GeneralizedKirkwood type="370" charge="0.06720" shct="0.72" />
<GeneralizedKirkwood type="377" charge="-0.60712" shct="0.85" /> <GeneralizedKirkwood type="371" charge="0.12287" shct="0.85" />
<GeneralizedKirkwood type="377" charge="-0.60712" shct="0.85" /> <GeneralizedKirkwood type="372" charge="0.07060" shct="0.72" />
<GeneralizedKirkwood type="378" charge="1.02369" shct="0.86" /> <GeneralizedKirkwood type="373" charge="0.10297" shct="0.85" />
<GeneralizedKirkwood type="379" charge="-0.87686" shct="0.85" /> <GeneralizedKirkwood type="374" charge="-0.10232" shct="0.72" />
<GeneralizedKirkwood type="380" charge="-0.51966" shct="0.85" /> <GeneralizedKirkwood type="375" charge="0.10225" shct="0.85" />
<GeneralizedKirkwood type="381" charge="0.25983" shct="0.85" /> <GeneralizedKirkwood type="376" charge="0.09833" shct="0.85" />
<GeneralizedKirkwood type="382" charge="1.00000" shct="0.8" /> <GeneralizedKirkwood type="377" charge="-0.53467" shct="0.85" />
<GeneralizedKirkwood type="383" charge="1.00000" shct="0.8" /> <GeneralizedKirkwood type="378" charge="0.90070" shct="0.86" />
<GeneralizedKirkwood type="384" charge="1.00000" shct="0.8" /> <GeneralizedKirkwood type="379" charge="-0.62196" shct="0.85" />
<GeneralizedKirkwood type="385" charge="1.00000" shct="0.8" /> <GeneralizedKirkwood type="380" charge="-0.53491" shct="0.85" />
<GeneralizedKirkwood type="386" charge="1.00000" shct="0.8" /> <GeneralizedKirkwood type="380" charge="-0.53491" shct="0.85" />
<GeneralizedKirkwood type="387" charge="2.00000" shct="0.8" /> <GeneralizedKirkwood type="381" charge="0.34636" shct="0.85" />
<GeneralizedKirkwood type="388" charge="2.00000" shct="0.8" /> <GeneralizedKirkwood type="381" charge="0.34636" shct="0.85" />
<GeneralizedKirkwood type="389" charge="2.00000" shct="0.8" /> <GeneralizedKirkwood type="381" charge="0.34636" shct="0.85" />
<GeneralizedKirkwood type="390" charge="-1.00000" shct="0.8" /> <GeneralizedKirkwood type="382" charge="-0.58166" shct="0.85" />
<GeneralizedKirkwood type="382" charge="-0.58166" shct="0.85" />
<GeneralizedKirkwood type="383" charge="1.02369" shct="0.86" />
<GeneralizedKirkwood type="384" charge="-0.87686" shct="0.85" />
<GeneralizedKirkwood type="385" charge="-0.50819" shct="0.85" />
<GeneralizedKirkwood type="385" charge="-0.50819" shct="0.85" />
<GeneralizedKirkwood type="386" charge="0.29418" shct="0.85" />
<GeneralizedKirkwood type="386" charge="0.29418" shct="0.85" />
<GeneralizedKirkwood type="387" charge="-0.60712" shct="0.85" />
<GeneralizedKirkwood type="387" charge="-0.60712" shct="0.85" />
<GeneralizedKirkwood type="388" charge="1.02369" shct="0.86" />
<GeneralizedKirkwood type="389" charge="-0.87686" shct="0.85" />
<GeneralizedKirkwood type="390" charge="0.90070" shct="0.86" />
<GeneralizedKirkwood type="391" charge="-0.62196" shct="0.85" />
<GeneralizedKirkwood type="392" charge="-0.53491" shct="0.85" />
<GeneralizedKirkwood type="392" charge="-0.53491" shct="0.85" />
<GeneralizedKirkwood type="393" charge="0.34636" shct="0.85" />
<GeneralizedKirkwood type="393" charge="0.34636" shct="0.85" />
<GeneralizedKirkwood type="394" charge="-0.58166" shct="0.85" />
<GeneralizedKirkwood type="394" charge="-0.58166" shct="0.85" />
<GeneralizedKirkwood type="395" charge="1.02369" shct="0.86" />
<GeneralizedKirkwood type="396" charge="-0.87686" shct="0.85" />
<GeneralizedKirkwood type="397" charge="-0.50819" shct="0.85" />
<GeneralizedKirkwood type="397" charge="-0.50819" shct="0.85" />
<GeneralizedKirkwood type="398" charge="0.29418" shct="0.85" />
<GeneralizedKirkwood type="398" charge="0.29418" shct="0.85" />
<GeneralizedKirkwood type="399" charge="-0.60712" shct="0.85" />
<GeneralizedKirkwood type="399" charge="-0.60712" shct="0.85" />
<GeneralizedKirkwood type="400" charge="1.02369" shct="0.86" />
<GeneralizedKirkwood type="401" charge="-0.87686" shct="0.85" />
<GeneralizedKirkwood type="402" charge="-0.51966" shct="0.85" />
<GeneralizedKirkwood type="403" charge="0.25983" shct="0.85" />
<GeneralizedKirkwood type="404" charge="1.00000" shct="0.8" />
<GeneralizedKirkwood type="405" charge="1.00000" shct="0.8" />
<GeneralizedKirkwood type="406" charge="1.00000" shct="0.8" />
<GeneralizedKirkwood type="407" charge="1.00000" shct="0.8" />
<GeneralizedKirkwood type="408" charge="1.00000" shct="0.8" />
<GeneralizedKirkwood type="409" charge="2.00000" shct="0.8" />
<GeneralizedKirkwood type="410" charge="2.00000" shct="0.8" />
<GeneralizedKirkwood type="411" charge="2.00000" shct="0.8" />
<GeneralizedKirkwood type="412" charge="2.00000" shct="0.8" />
<GeneralizedKirkwood type="413" charge="-1.00000" shct="0.8" />
</AmoebaGeneralizedKirkwoodForce> </AmoebaGeneralizedKirkwoodForce>
<AmoebaWcaDispersionForce epso="0.46024" epsh="0.056484" rmino="0.17025" rminh="0.13275" awater="33.428" slevy="1.0" dispoff="0.026" shctd="0.81" > <AmoebaWcaDispersionForce epso="0.46024" epsh="0.056484" rmino="0.17025" rminh="0.13275" awater="33.428" slevy="1.0" dispoff="0.026" shctd="0.81" >
<WcaDispersion class="1" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="1" radius="0.1855" epsilon="0.46024" />
<WcaDispersion class="2" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="2" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="3" radius="0.191" epsilon="0.443504" /> <WcaDispersion class="3" radius="0.191" epsilon="0.443504" />
<WcaDispersion class="4" radius="0.1295" epsilon="0.092048" /> <WcaDispersion class="4" radius="0.1295" epsilon="0.092048" />
<WcaDispersion class="5" radius="0.165" epsilon="0.468608" /> <WcaDispersion class="5" radius="0.165" epsilon="0.468608" />
<WcaDispersion class="6" radius="0.147" epsilon="0.108784" /> <WcaDispersion class="6" radius="0.147" epsilon="0.108784" />
<WcaDispersion class="7" radius="0.1825" epsilon="0.422584" /> <WcaDispersion class="7" radius="0.1825" epsilon="0.422584" />
<WcaDispersion class="8" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="8" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="9" radius="0.149" epsilon="0.100416" /> <WcaDispersion class="9" radius="0.149" epsilon="0.100416" />
<WcaDispersion class="10" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="10" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="11" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="11" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="12" radius="0.1955" epsilon="1.61084" /> <WcaDispersion class="12" radius="0.1955" epsilon="1.61084" />
<WcaDispersion class="13" radius="0.15" epsilon="0.110876" /> <WcaDispersion class="13" radius="0.15" epsilon="0.110876" />
<WcaDispersion class="15" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="14" radius="0.2175" epsilon="1.61084" />
<WcaDispersion class="16" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="15" radius="0.1855" epsilon="0.46024" />
<WcaDispersion class="17" radius="0.19" epsilon="0.372376" /> <WcaDispersion class="16" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="18" radius="0.149" epsilon="0.108784" /> <WcaDispersion class="17" radius="0.19" epsilon="0.372376" />
<WcaDispersion class="19" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="18" radius="0.149" epsilon="0.108784" />
<WcaDispersion class="20" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="19" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="22" radius="0.19" epsilon="0.422584" /> <WcaDispersion class="20" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="23" radius="0.149" epsilon="0.108784" /> <WcaDispersion class="21" radius="0.166" epsilon="0.468608" />
<WcaDispersion class="24" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="22" radius="0.19" epsilon="0.422584" />
<WcaDispersion class="25" radius="0.1295" epsilon="0.092048" /> <WcaDispersion class="23" radius="0.149" epsilon="0.108784" />
<WcaDispersion class="26" radius="0.19" epsilon="0.422584" /> <WcaDispersion class="24" radius="0.1855" epsilon="0.46024" />
<WcaDispersion class="27" radius="0.149" epsilon="0.108784" /> <WcaDispersion class="25" radius="0.1295" epsilon="0.092048" />
<WcaDispersion class="28" radius="0.19" epsilon="0.422584" /> <WcaDispersion class="26" radius="0.19" epsilon="0.422584" />
<WcaDispersion class="29" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="27" radius="0.149" epsilon="0.108784" />
<WcaDispersion class="30" radius="0.191" epsilon="0.443504" /> <WcaDispersion class="28" radius="0.19" epsilon="0.422584" />
<WcaDispersion class="31" radius="0.1725" epsilon="0.468608" /> <WcaDispersion class="29" radius="0.1855" epsilon="0.46024" />
<WcaDispersion class="32" radius="0.165" epsilon="0.468608" /> <WcaDispersion class="30" radius="0.191" epsilon="0.443504" />
<WcaDispersion class="33" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="31" radius="0.1725" epsilon="0.468608" />
<WcaDispersion class="34" radius="0.13275" epsilon="0.06276" /> <WcaDispersion class="32" radius="0.165" epsilon="0.468608" />
<WcaDispersion class="35" radius="0.1855" epsilon="0.43932" /> <WcaDispersion class="33" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="36" radius="0.124" epsilon="0.075312" /> <WcaDispersion class="34" radius="0.13275" epsilon="0.06276" />
<WcaDispersion class="38" radius="0.121" epsilon="0.08368" /> <WcaDispersion class="35" radius="0.1855" epsilon="0.43932" />
<WcaDispersion class="39" radius="0.1825" epsilon="0.422584" /> <WcaDispersion class="36" radius="0.124" epsilon="0.075312" />
<WcaDispersion class="40" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="37" radius="0.135" epsilon="0.08368" />
<WcaDispersion class="41" radius="0.1855" epsilon="0.43932" /> <WcaDispersion class="38" radius="0.121" epsilon="0.08368" />
<WcaDispersion class="42" radius="0.124" epsilon="0.075312" /> <WcaDispersion class="39" radius="0.1825" epsilon="0.422584" />
<WcaDispersion class="43" radius="0.184" epsilon="0.43932" /> <WcaDispersion class="40" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="44" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="41" radius="0.1855" epsilon="0.43932" />
<WcaDispersion class="45" radius="0.175" epsilon="0.422584" /> <WcaDispersion class="42" radius="0.124" epsilon="0.075312" />
<WcaDispersion class="46" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="43" radius="0.184" epsilon="0.43932" />
<WcaDispersion class="47" radius="0.175" epsilon="0.43932" /> <WcaDispersion class="44" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="48" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="45" radius="0.175" epsilon="0.422584" />
<WcaDispersion class="49" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="46" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="50" radius="0.13" epsilon="0.075312" /> <WcaDispersion class="47" radius="0.175" epsilon="0.43932" />
<WcaDispersion class="51" radius="0.175" epsilon="0.422584" /> <WcaDispersion class="48" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="52" radius="0.1275" epsilon="0.079496" /> <WcaDispersion class="49" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="53" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="50" radius="0.13" epsilon="0.075312" />
<WcaDispersion class="54" radius="0.189" epsilon="0.422584" /> <WcaDispersion class="51" radius="0.175" epsilon="0.422584" />
<WcaDispersion class="55" radius="0.165" epsilon="0.468608" /> <WcaDispersion class="52" radius="0.1275" epsilon="0.079496" />
<WcaDispersion class="56" radius="0.14" epsilon="0.100416" /> <WcaDispersion class="53" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="57" radius="0.14" epsilon="0.100416" /> <WcaDispersion class="54" radius="0.189" epsilon="0.422584" />
<WcaDispersion class="58" radius="0.175" epsilon="0.43932" /> <WcaDispersion class="55" radius="0.165" epsilon="0.468608" />
<WcaDispersion class="59" radius="0.115" epsilon="0.0422584" /> <WcaDispersion class="56" radius="0.14" epsilon="0.100416" />
<WcaDispersion class="60" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="57" radius="0.14" epsilon="0.100416" />
<WcaDispersion class="61" radius="0.149" epsilon="0.100416" /> <WcaDispersion class="58" radius="0.175" epsilon="0.43932" />
<WcaDispersion class="62" radius="0.17025" epsilon="0.468608" /> <WcaDispersion class="59" radius="0.115" epsilon="0.0422584" />
<WcaDispersion class="63" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="60" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="64" radius="0.149" epsilon="0.100416" /> <WcaDispersion class="61" radius="0.149" epsilon="0.100416" />
<WcaDispersion class="65" radius="0.149" epsilon="0.100416" /> <WcaDispersion class="62" radius="0.17025" epsilon="0.468608" />
<WcaDispersion class="66" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="63" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="67" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="64" radius="0.149" epsilon="0.100416" />
<WcaDispersion class="68" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="65" radius="0.149" epsilon="0.100416" />
<WcaDispersion class="69" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="66" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="70" radius="0.2225" epsilon="1.63176" /> <WcaDispersion class="67" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="71" radius="0.168" epsilon="0.468608" /> <WcaDispersion class="68" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="72" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="69" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="73" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="70" radius="0.2225" epsilon="1.63176" />
<WcaDispersion class="74" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="71" radius="0.168" epsilon="0.468608" />
<WcaDispersion class="75" radius="0.119" epsilon="0.33472" /> <WcaDispersion class="72" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="76" radius="0.151" epsilon="1.08784" /> <WcaDispersion class="73" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="77" radius="0.1855" epsilon="1.4644" /> <WcaDispersion class="74" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="78" radius="0.207" epsilon="1.84096" /> <WcaDispersion class="75" radius="0.119" epsilon="0.33472" />
<WcaDispersion class="79" radius="0.2185" epsilon="2.21752" /> <WcaDispersion class="76" radius="0.151" epsilon="1.08784" />
<WcaDispersion class="80" radius="0.094" epsilon="0.380744" /> <WcaDispersion class="77" radius="0.1855" epsilon="1.4644" />
<WcaDispersion class="81" radius="0.1275" epsilon="3.5564" /> <WcaDispersion class="78" radius="0.207" epsilon="1.84096" />
<WcaDispersion class="82" radius="0.1565" epsilon="6.6944" /> <WcaDispersion class="79" radius="0.2185" epsilon="2.21752" />
<WcaDispersion class="83" radius="0.2065" epsilon="1.42256" /> <WcaDispersion class="80" radius="0.094" epsilon="0.380744" />
<WcaDispersion class="14" radius="0.2175" epsilon="1.61084" /> <WcaDispersion class="81" radius="0.147" epsilon="1.2552" />
<WcaDispersion class="21" radius="0.166" epsilon="0.468608" /> <WcaDispersion class="82" radius="0.1815" epsilon="1.4644" />
<WcaDispersion class="37" radius="0.135" epsilon="0.08368" /> <WcaDispersion class="83" radius="0.134" epsilon="0.928848" />
<WcaDispersion class="84" radius="0.2065" epsilon="1.42256" />
</AmoebaWcaDispersionForce> </AmoebaWcaDispersionForce>
</ForceField> </ForceField>
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 4d32047c
...@@ -2625,7 +2625,7 @@ class AmoebaPiTorsionGenerator: ...@@ -2625,7 +2625,7 @@ class AmoebaPiTorsionGenerator:
atom1 = bond.atom1 atom1 = bond.atom1
atom2 = bond.atom2 atom2 = bond.atom2
if (len(data.atomBonds[atom1]) == 3 and len(data.atomBonds[atom1]) == 3): if (len(data.atomBonds[atom1]) == 3 and len(data.atomBonds[atom2]) == 3):
type1 = data.atomType[data.atoms[atom1]] type1 = data.atomType[data.atoms[atom1]]
type2 = data.atomType[data.atoms[atom2]] type2 = data.atomType[data.atoms[atom2]]
...@@ -2910,7 +2910,7 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2910,7 +2910,7 @@ class AmoebaTorsionTorsionGenerator:
# match in reverse order # match in reverse order
if (type5 in types1 and type4 in types2 and type3 in types3 and type2 in types4 and type1 in types5): elif (type5 in types1 and type4 in types2 and type3 in types3 and type2 in types4 and type1 in types5):
chiralAtomIndex = self.getChiralAtomIndex(data, sys, ib, ic, id) chiralAtomIndex = self.getChiralAtomIndex(data, sys, ib, ic, id)
force.addTorsionTorsion(ie, id, ic, ib, ia, chiralAtomIndex, self.gridIndex[i]) force.addTorsionTorsion(ie, id, ic, ib, ia, chiralAtomIndex, self.gridIndex[i])
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment