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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
# biotype 2006 CA "Calcium Ion" 256
# biotype 2007 CL "Chloride Ion" 258
ions = { 'Li+' : [ 'LI', 249, 249 ],
'Na+' : [ 'NA', 250, 2003 ],
'K+' : [ 'K', 251, 2004 ],
'Rb+' : [ 'RB', 252, 252 ],
'Cs+' : [ 'CS', 253, 253 ],
'Be+' : [ 'BE', 254, 254 ],
'Mg+' : [ 'MG', 255, 2005 ],
'Ca+' : [ 'CA', 256, 2006 ],
'Zn+' : [ 'ZN', 257, 257 ],
'Cl-' : [ 'Cl', 258, 2007 ]
ions = { 'Li+' : ['LI', 249],
'Na+' : ['NA', 250],
'K+' : ['K', 251],
'Rb+' : ['RB', 252],
'Cs+' : ['CS', 253],
'Be+' : ['BE', 254],
'Mg+' : ['MG', 255],
'Ca+' : ['CA', 256],
'Zn+' : ['ZN', 257],
'Cl-' : ['Cl', 258]
}
atomTypes = {}
......@@ -339,34 +339,23 @@ def buildResidueDict( residueXmlFileName ):
def setBioTypes( bioTypes, residueDict ):
for res in residueDict.values():
for resname, res in residueDict.items():
for atom in res['atoms']:
atomLookup = res['atoms'][atom]['tinkerLookupName']
resLookup = [res['tinkerLookupName']]
resLookup = []
if res['type'] == 'dna':
if res['loc'] in ('5', 'N'):
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'):
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")
if res['type'] == 'rna':
if res['loc'] in ('5', 'N'):
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'):
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(res['tinkerLookupName'])
for suffix in resLookup:
lookupName = atomLookup+'_'+suffix
if lookupName in bioTypes:
......@@ -556,6 +545,7 @@ while lineIndex < len( allLines ):
if( fields[3] in ions ):
ionInfo = ions[fields[3]]
element = ionInfo[0]
ionInfo[1] = int(fields[1])
else:
element = fields[3][0]
atomTypes[int(fields[1])] = (fields[2], element, fields[6])
......@@ -564,6 +554,9 @@ while lineIndex < len( allLines ):
elif fields[0] == 'biotype':
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:]
lineIndex += 1
......@@ -840,24 +833,26 @@ if( isAmoeba ):
# AmoebaTorsionForce
torsionUnit = float(scalars['torsionunit'])
outputString = """ <AmoebaTorsionForce torsionUnit="%s">""" % ( torsionUnit )
outputString = """ <PeriodicTorsionForce>"""
tinkerXmlFile.write( "%s\n" % (outputString ) )
torsions = forces['torsion']
conversion = 4.184*torsionUnit
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
for ii in range(0,3):
torsionSuffix = str(ii+1)
amplitudeAttributeName = 'amp' + torsionSuffix
angleAttributeName = 'angle' + torsionSuffix
amplitudeAttributeName = 'k'+torsionSuffix
angleAttributeName = 'phase'+torsionSuffix
periodicityAttributeName = 'periodicity'+torsionSuffix
amplitude = float(torsion[startIndex])*conversion
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
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 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -973,7 +973,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1017,7 +1017,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1041,7 +1041,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1085,7 +1085,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1109,7 +1109,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1149,7 +1149,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1173,7 +1173,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1217,7 +1217,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1239,7 +1239,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1280,7 +1280,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1302,7 +1302,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1343,7 +1343,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1365,7 +1365,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1402,7 +1402,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1424,7 +1424,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1465,7 +1465,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1490,7 +1490,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1535,7 +1535,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1560,7 +1560,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1605,7 +1605,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1630,7 +1630,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1671,7 +1671,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1696,7 +1696,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1741,7 +1741,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1765,7 +1765,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1808,7 +1808,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1832,7 +1832,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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"/>
......@@ -1875,7 +1875,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1899,7 +1899,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -1938,7 +1938,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -1962,7 +1962,7 @@
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<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'"/>
......@@ -2005,7 +2005,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2075,7 +2075,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2145,7 +2145,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2211,7 +2211,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2281,7 +2281,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2346,7 +2346,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<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*"/>
......@@ -2411,7 +2411,7 @@
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
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......@@ -2472,7 +2472,7 @@
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......@@ -2537,7 +2537,7 @@
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......@@ -2609,7 +2609,7 @@
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......@@ -2681,7 +2681,7 @@
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......@@ -2749,7 +2749,7 @@
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......@@ -2821,7 +2821,7 @@
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......@@ -2884,7 +2884,7 @@
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......@@ -2947,7 +2947,7 @@
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......@@ -3006,7 +3006,7 @@
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......
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
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<Info>
<Source>amoebabio09.prm</Source>
<DateGenerated>2015-11-19</DateGenerated>
<Reference></Reference>
</Info>
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