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Commit 69d7dc4f authored by peastman's avatar peastman
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Hopefully finished with supporting nucleotides in AMOEBA

parent 4daa1acb
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Showing with 11771 additions and 9434 deletions
devtools/forcefield-scripts/processTinkerForceField.py
View file @ 69d7dc4f
...@@ -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 = {}
...@@ -339,34 +339,23 @@ def buildResidueDict( residueXmlFileName ): ...@@ -339,34 +339,23 @@ def buildResidueDict( residueXmlFileName ):
def setBioTypes( bioTypes, residueDict ): def setBioTypes( bioTypes, residueDict ):
for res in residueDict.values(): for resname, res in residueDict.items():
for atom in res['atoms']: for atom in res['atoms']:
atomLookup = res['atoms'][atom]['tinkerLookupName'] atomLookup = res['atoms'][atom]['tinkerLookupName']
resLookup = [res['tinkerLookupName']] resLookup = []
if res['type'] == 'dna': if res['type'] == 'dna':
if res['loc'] in ('5', 'N'): if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl DNA") resLookup.append("5'-Hydroxyl DNA")
resLookup.append("5'-Phosphate OS DNA")
resLookup.append("5'-Phosphate P DNA")
resLookup.append("5'-Phosphate OP DNA")
if res['loc'] in ('3', 'N'): if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl DNA") resLookup.append("3'-Hydroxyl DNA")
resLookup.append("3'-Phosphate OS DNA")
resLookup.append("3'-Phosphate P DNA")
resLookup.append("3'-Phosphate OP DNA")
resLookup.append("Phosphodiester DNA") resLookup.append("Phosphodiester DNA")
if res['type'] == 'rna': if res['type'] == 'rna':
if res['loc'] in ('5', 'N'): if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl RNA") resLookup.append("5'-Hydroxyl RNA")
resLookup.append("5'-Phosphate OS RNA")
resLookup.append("5'-Phosphate P RNA")
resLookup.append("5'-Phosphate OP RNA")
if res['loc'] in ('3', 'N'): if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl RNA") resLookup.append("3'-Hydroxyl RNA")
resLookup.append("3'-Phosphate OS RNA")
resLookup.append("3'-Phosphate P RNA")
resLookup.append("3'-Phosphate OP RNA")
resLookup.append("Phosphodiester RNA") resLookup.append("Phosphodiester RNA")
resLookup.append(res['tinkerLookupName'])
for suffix in resLookup: for suffix in resLookup:
lookupName = atomLookup+'_'+suffix lookupName = atomLookup+'_'+suffix
if lookupName in bioTypes: if lookupName in bioTypes:
...@@ -556,6 +545,7 @@ while lineIndex < len( allLines ): ...@@ -556,6 +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])
...@@ -564,6 +554,9 @@ while lineIndex < len( allLines ): ...@@ -564,6 +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
...@@ -840,24 +833,26 @@ if( isAmoeba ): ...@@ -840,24 +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" )
#============================================================================================= #=============================================================================================
......
devtools/forcefield-scripts/residuesFinal.xml
View file @ 69d7dc4f
...@@ -949,7 +949,7 @@ ...@@ -949,7 +949,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -973,7 +973,7 @@ ...@@ -973,7 +973,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -1017,7 +1017,7 @@ ...@@ -1017,7 +1017,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1041,7 +1041,7 @@ ...@@ -1041,7 +1041,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -1085,7 +1085,7 @@ ...@@ -1085,7 +1085,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1109,7 +1109,7 @@ ...@@ -1109,7 +1109,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -1149,7 +1149,7 @@ ...@@ -1149,7 +1149,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1173,7 +1173,7 @@ ...@@ -1173,7 +1173,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -1217,7 +1217,7 @@ ...@@ -1217,7 +1217,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1239,7 +1239,7 @@ ...@@ -1239,7 +1239,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -1280,7 +1280,7 @@ ...@@ -1280,7 +1280,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1302,7 +1302,7 @@ ...@@ -1302,7 +1302,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -1343,7 +1343,7 @@ ...@@ -1343,7 +1343,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1365,7 +1365,7 @@ ...@@ -1365,7 +1365,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -1402,7 +1402,7 @@ ...@@ -1402,7 +1402,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1424,7 +1424,7 @@ ...@@ -1424,7 +1424,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -1465,7 +1465,7 @@ ...@@ -1465,7 +1465,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1490,7 +1490,7 @@ ...@@ -1490,7 +1490,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -1535,7 +1535,7 @@ ...@@ -1535,7 +1535,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1560,7 +1560,7 @@ ...@@ -1560,7 +1560,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -1605,7 +1605,7 @@ ...@@ -1605,7 +1605,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1630,7 +1630,7 @@ ...@@ -1630,7 +1630,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -1671,7 +1671,7 @@ ...@@ -1671,7 +1671,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1696,7 +1696,7 @@ ...@@ -1696,7 +1696,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -1741,7 +1741,7 @@ ...@@ -1741,7 +1741,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1765,7 +1765,7 @@ ...@@ -1765,7 +1765,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -1808,7 +1808,7 @@ ...@@ -1808,7 +1808,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1832,7 +1832,7 @@ ...@@ -1832,7 +1832,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -1875,7 +1875,7 @@ ...@@ -1875,7 +1875,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1899,7 +1899,7 @@ ...@@ -1899,7 +1899,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -1938,7 +1938,7 @@ ...@@ -1938,7 +1938,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -1962,7 +1962,7 @@ ...@@ -1962,7 +1962,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/> <Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2*"/> <Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -2005,7 +2005,7 @@ ...@@ -2005,7 +2005,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2075,7 +2075,7 @@ ...@@ -2075,7 +2075,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2145,7 +2145,7 @@ ...@@ -2145,7 +2145,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2211,7 +2211,7 @@ ...@@ -2211,7 +2211,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2281,7 +2281,7 @@ ...@@ -2281,7 +2281,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2346,7 +2346,7 @@ ...@@ -2346,7 +2346,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2411,7 +2411,7 @@ ...@@ -2411,7 +2411,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2472,7 +2472,7 @@ ...@@ -2472,7 +2472,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2537,7 +2537,7 @@ ...@@ -2537,7 +2537,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2609,7 +2609,7 @@ ...@@ -2609,7 +2609,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2681,7 +2681,7 @@ ...@@ -2681,7 +2681,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2749,7 +2749,7 @@ ...@@ -2749,7 +2749,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2821,7 +2821,7 @@ ...@@ -2821,7 +2821,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2884,7 +2884,7 @@ ...@@ -2884,7 +2884,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -2947,7 +2947,7 @@ ...@@ -2947,7 +2947,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
...@@ -3006,7 +3006,7 @@ ...@@ -3006,7 +3006,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/> <Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/> <Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/> <Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5*"/> <Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/> <Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/> <Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/> <Atom name="O4'" tinkerLookupName="O4*"/>
......
wrappers/python/simtk/openmm/app/data/amoeba2009.xml
View file @ 69d7dc4f
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 @ 69d7dc4f
<ForceField> <ForceField>
<AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" dielectricOffset="0.009" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663"> <Info>
<Source>amoebabio09.prm</Source>
<DateGenerated>2015-11-19</DateGenerated>
<Reference></Reference>
</Info>
<AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
<GeneralizedKirkwood type="1" charge="-0.22620" shct="0.79" /> <GeneralizedKirkwood type="1" charge="-0.22620" shct="0.79" />
<GeneralizedKirkwood type="2" charge="-0.15245" shct="0.72" /> <GeneralizedKirkwood type="2" charge="-0.15245" shct="0.72" />
<GeneralizedKirkwood type="2" charge="-0.26188" shct="0.72" /> <GeneralizedKirkwood type="2" charge="-0.26188" shct="0.72" />
<GeneralizedKirkwood type="2" charge="-0.06378" shct="0.72" />
<GeneralizedKirkwood type="2" charge="-0.00060" shct="0.72" /> <GeneralizedKirkwood type="2" charge="-0.00060" shct="0.72" />
<GeneralizedKirkwood type="2" charge="-0.15431" shct="0.72" />
<GeneralizedKirkwood type="3" charge="0.84374" shct="0.72" /> <GeneralizedKirkwood type="3" charge="0.84374" shct="0.72" />
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...@@ -13,7 +20,9 @@ ...@@ -13,7 +20,9 @@
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...@@ -42,6 +51,7 @@ ...@@ -42,6 +51,7 @@
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...@@ -71,6 +81,7 @@ ...@@ -71,6 +81,7 @@
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...@@ -84,6 +95,7 @@ ...@@ -84,6 +95,7 @@
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...@@ -190,14 +202,12 @@ ...@@ -190,14 +202,12 @@
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...@@ -211,253 +221,284 @@ ...@@ -211,253 +221,284 @@
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<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" />
...@@ -473,12 +514,14 @@ ...@@ -473,12 +514,14 @@
<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="14" radius="0.2175" epsilon="1.61084" />
<WcaDispersion class="15" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="15" radius="0.1855" epsilon="0.46024" />
<WcaDispersion class="16" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="16" radius="0.191" epsilon="0.422584" />
<WcaDispersion class="17" radius="0.19" epsilon="0.372376" /> <WcaDispersion class="17" radius="0.19" epsilon="0.372376" />
<WcaDispersion class="18" radius="0.149" epsilon="0.108784" /> <WcaDispersion class="18" radius="0.149" epsilon="0.108784" />
<WcaDispersion class="19" radius="0.17025" epsilon="0.46024" /> <WcaDispersion class="19" radius="0.17025" epsilon="0.46024" />
<WcaDispersion class="20" radius="0.13275" epsilon="0.056484" /> <WcaDispersion class="20" radius="0.13275" epsilon="0.056484" />
<WcaDispersion class="21" radius="0.166" epsilon="0.468608" />
<WcaDispersion class="22" radius="0.19" epsilon="0.422584" /> <WcaDispersion class="22" radius="0.19" epsilon="0.422584" />
<WcaDispersion class="23" radius="0.149" epsilon="0.108784" /> <WcaDispersion class="23" radius="0.149" epsilon="0.108784" />
<WcaDispersion class="24" radius="0.1855" epsilon="0.46024" /> <WcaDispersion class="24" radius="0.1855" epsilon="0.46024" />
...@@ -494,6 +537,7 @@ ...@@ -494,6 +537,7 @@
<WcaDispersion class="34" radius="0.13275" epsilon="0.06276" /> <WcaDispersion class="34" radius="0.13275" epsilon="0.06276" />
<WcaDispersion class="35" radius="0.1855" epsilon="0.43932" /> <WcaDispersion class="35" radius="0.1855" epsilon="0.43932" />
<WcaDispersion class="36" radius="0.124" epsilon="0.075312" /> <WcaDispersion class="36" radius="0.124" epsilon="0.075312" />
<WcaDispersion class="37" radius="0.135" epsilon="0.08368" />
<WcaDispersion class="38" radius="0.121" epsilon="0.08368" /> <WcaDispersion class="38" radius="0.121" epsilon="0.08368" />
<WcaDispersion class="39" radius="0.1825" epsilon="0.422584" /> <WcaDispersion class="39" radius="0.1825" epsilon="0.422584" />
<WcaDispersion class="40" radius="0.191" epsilon="0.422584" /> <WcaDispersion class="40" radius="0.191" epsilon="0.422584" />
...@@ -537,11 +581,9 @@ ...@@ -537,11 +581,9 @@
<WcaDispersion class="78" radius="0.207" epsilon="1.84096" /> <WcaDispersion class="78" radius="0.207" epsilon="1.84096" />
<WcaDispersion class="79" radius="0.2185" epsilon="2.21752" /> <WcaDispersion class="79" radius="0.2185" epsilon="2.21752" />
<WcaDispersion class="80" radius="0.094" epsilon="0.380744" /> <WcaDispersion class="80" radius="0.094" epsilon="0.380744" />
<WcaDispersion class="81" radius="0.1275" epsilon="3.5564" /> <WcaDispersion class="81" radius="0.147" epsilon="1.2552" />
<WcaDispersion class="82" radius="0.1565" epsilon="6.6944" /> <WcaDispersion class="82" radius="0.1815" epsilon="1.4644" />
<WcaDispersion class="83" radius="0.2065" epsilon="1.42256" /> <WcaDispersion class="83" radius="0.134" epsilon="0.928848" />
<WcaDispersion class="14" radius="0.2175" epsilon="1.61084" /> <WcaDispersion class="84" radius="0.2065" epsilon="1.42256" />
<WcaDispersion class="21" radius="0.166" epsilon="0.468608" />
<WcaDispersion class="37" radius="0.135" epsilon="0.08368" />
</AmoebaWcaDispersionForce> </AmoebaWcaDispersionForce>
</ForceField> </ForceField>
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