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petermr  committed cee4e48 Draft

passes legacy tests

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  • Parent commits 237f7e9

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Files changed (57)

File src/main/resources/cml/chemistry/classList.xml

-<classList>
-	<class tag="arrayTool"    name="org.xmlcml.cml.chemistry.ArrayToolVisitable" />
-	<class tag="atomTypeTool" name="org.xmlcml.cml.chemistry.AtomTypeToolVisitable" />
-	<class tag="energy"       name="org.xmlcml.cml.chemistry.EnergyVisitable" />
-	<class tag="geometry"     name="org.xmlcml.cml.chemistry.GeometryVisitable" />
-	<class tag="moleculeTool" name="org.xmlcml.cml.chemistry.MoleculeToolVisitable" />
-	<class tag="units"        name="org.xmlcml.cml.units.UnitsVisitor" />
-</classList>
-		

File src/main/resources/cml/examples/amberAssert.xml

-<cml:computation xmlns="http://www.xml-cml.org/semanticforcefields"
-	xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:cml="http://www.xml-cml.org/schema"
-	xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-
-	<cml:molecule id="molecule" href="src/test/resources/org/xmlcml/cml/forcefield/aceticCompute.xml" />
-	<list id="parm94Test" href="src/main/resources/org/xmlcml/cml/forcefield/amber/parm94test.xml"/>
-	<!--  add hash based on atomType children -->
-	<visitor
-		xpath="//cml:list[@id='parm94Test']/cml:list/cml:list[count(cml:atomType)>0]" method="addHash" args="./cml:atomType"/>
-
-<!-- molecule must have atoms -->
-	<assert validity="false" count="0"
-		xpath="//cml:molecule[@id='molecule']/cml:atomArray/cml:atom"/>
-		
-<!--  must have 3D coords -->
-	<assert xpath="//cml:molecule[@id='molecule']/cml:atom[not(@x3)] |
-		           //cml:molecule[@id='molecule']/cml:atom[not(@y3)] |
-		           //cml:molecule[@id='molecule']/cml:atom[not(@z3)] " 
-		       count="0"/>
-
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateBonds"/>
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond" method="addHash"/>
-<!-- molecule must have bonds -->
-	<assert count="7"
-		xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond"/>
-
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateBondOrders"/>
-<!-- molecule must have bond orders -->
-	<assert count="7"
-		xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond[@order]"/>
-
- 	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateAtomTypes"/>
-	<assert count="0"
-		xpath="//cml:molecule[@id='molecule']/cml:atomArray/cml:atom[not(cml:atomType[@dictRef='amber:parm94Type'])]"/>
-	<!--  add hash based on atomTypes of AtomRefs -->
-
-<!--  		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']/cml:bond" method="getBondParameters" ff="parm4"/>
-		
-	<moleculeTool
-		xpath="//cml:molecule/cml:bondArray/cml:bond" method="dictLookup"
-		list_id="parm94"
-		property_path="//cml:list[@id='amber']/cml:list[@title='bonds']/cml:list[@id='%i']" />
--->		
-		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateAngles"/>
-	<assert count="10"
-		xpath="//cml:molecule[@id='molecule']/cml:list/cml:angle"/>
-<!-- 		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']/cml:bond" method="getAngleParameters" ff="parm4"/>
--->		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateTorsions"/>
-	<assert count="8"
-		xpath="//cml:molecule[@id='molecule']/cml:list/cml:torsion"/>
-	<visitor
-		xpath="//cml:molecule[@id='molecule']//cml:*[@atomRefs2 | @atomRefs3 | @atomRefs4]" method="addAtomRefTypesHash"/>
-	<writer xpath="//cml:molecule[@id='molecule']" file="testAtomTypes.cml" /> 
-<!-- 		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']/cml:bond" method="getTorsionParameters" ff="parm4"/>
--->		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']" method="getOrCreateNonBonded"/>
-<!-- 		
-	<moleculeTool
-		xpath="//cml:molecule[@id='molecule']/cml:bond" method="getNonBondedParameters" ff="parm4"/>
-	
-	<singlePointEnergy forcefieldRef="//cml:list[@id='amber']" moleculeRef="//cml:molecule" />
-	<writer xpath="//cml:molecule" file="output/%i_output.cml" /> 
-	<directEnergyOptimisation forcefieldRef="//cml:list[@id='amber']" moleculeRef="//cml:molecule" n="1000"/>
-	<writer xpath="//cml:molecule" file="output/%i_optimised.cml" /> 
--->
-
-</cml:computation>

File src/main/resources/cml/examples/amberComputation.xml

-<computation xmlns="http://www.xml-cml.org/semanticcomputation"
-    xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:cml="http://www.xml-cml.org/schema"
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-    <visitor class="org.xmlcml.semantic.visitors.HREFVisitor"/>
-    <visitor class="org.xmlcml.cml.chemistry.SemanticChemistryClasses"/>
-    <visitor class="org.xmlcml.cml.chemistry.CMLClassDecorator"/>
-    <!-- 
-    <visitor class="org.xmlcml.semantic.visitors.ShowTreeVisitor"/>
--->
-    <queryNS prefix="semc"  uri="http://www.xml-cml.org/semanticcomputation"/>
-    <queryNS prefix="semf"  uri="http://www.xml-cml.org/semanticforcefields"/>
-    <queryNS prefix="cml"   uri="http://www.xml-cml.org/schema"/>
-    <queryNS prefix="m"     uri="http://www.w3.org/1998/Math/MathML"/>
-	<queryNS prefix="amber" uri="http://www.xml-cml.org/dict/amber:gaffType" />
-	<queryNS prefix="cmlx"  uri="http://www.xml-cml.org/schema/cmlx" />
-
-     <keyValue key="all"           value="/*" />
-     <keyValue key="mainff"        value="src/main/resources/org/xmlcml/cml/forcefield" />
-     <keyValue key="testff"        value="src/test/resources/org/xmlcml/cml/forcefield" />
-     <keyValue key="out"           value="output" />
-     <keyValue key="mol"           value="//cml:molecule[@id='molecule']" />
-     <keyValue key="molBondTop"    value="${mol}/cml:bondArray" />
-     <keyValue key="molBonds"      value="${molBondTop}/cml:bond" />
-     <keyValue key="molAngTop"     value="${mol}/cml:list[cml:angle]" />
-     <keyValue key="molAngs"       value="${molAngTop}/cml:angle" />
-     <keyValue key="molTorTop"     value="${mol}/cml:list[cml:torsion]" />
-     <keyValue key="molTors"       value="${molTorTop}/cml:torsion" />
-     <keyValue key="molNonBondTop" value="${mol}/cml:list[@id='createdNonBonded']" />
-     <keyValue key="molNonBonds"   value="${molNonBondTop}/cml:length" />
-     <keyValue key="parm"          value="//cml:list[@id='parm94Test']" />
-     <keyValue key="parmBondTop"   value="${parm}/cml:list[@dictRef='ff:bonds']" />
-     <keyValue key="parmAngTop"    value="${parm}/cml:list[@dictRef='ff:angles']" />
-     <keyValue key="parmTorTop"    value="${parm}/cml:list[@dictRef='ff:torsions']" />
-     <keyValue key="parmNonBond"   value="${parm}/cml:list[@dictRef='amber:mod_re']" />
-     <keyValue key="cmlProperty"   value="org.xmlcml.cml.element.CMLProperty" />  
-     
-     <cml:molecule id="molecule" href="${testff}/aceticStart.cml" />
-     
-     <writer xpath="${mol}" file="${out}/aceticStart.cml"/>
-     
-    <cml:list id="parm94Test" href="${mainff}/amber/parm94test.xml"/>
-<!--  add hash based on atomType children -->
-    <atomTypeTool method="addAtomTypesId" using="./cml:atomType"
-        xpath="${parm}/cml:list/cml:list[count(cml:atomType)>0]" />
-    
-    <unitsVisitor xpath="${parm}//cml:scalar[@dictRef='ff:angeq' or @dictRef='ff:phase']" method="degrees2Radians"/>
-    
-    <writer xpath="${parm}" file="${out}/parm94testNew.xml" /> 
-
-
-
-<!-- === create/ensure bonds, angles, torsions, nonbonded and then hash atom types === -->
-
-    <writer xpath="${mol}" file="${out}/initialTemplate.xml" /> 
-    
-<!-- =========== copy parameters to bonds and tidy ============== -->
-
-    <xpathVisitor id="bonds.addProperty" method="addChild"         xpath="${molBonds}" args="${cmlProperty}"/>
-    <atomTypeTool method="addAtomTypesId"   xpath="${molBonds}"/>
-    <writer xpath="${all}" file="${out}/initialBonds00.xml" /> 
-    <xpathVisitor id="bonds.copyFunctionalForm" method="copyChild" xpath="${molBondTop}" 
-            from="${parmBondTop}/semf:functionalForm" />
-    <writer xpath="${all}" file="${out}/initialBonds0.xml" /> 
-    <xpathVisitor id="bonds.copyAtoms" method="copyChild"        xpath="${molBonds}/cml:property" join="../@cmlx:atomTypesId"
-            from="${parmBondTop}" using="./cml:list[@cmlx:atomTypesId='${join.value}']" />
-
-    <writer xpath="${mol}" file="${out}/initialBonds.xml" /> 
-         
-<!-- =========== copy parameters to angles and tidy ============== -->
-<!-- 
-    <moleculeTool method="getOrCreateAngles"      xpath="${mol}" setId="createdAngles" />
-    <xpathVisitor method="addChild"        xpath="${molAngs}" args="${cmlProperty}"/>
-    <atomTypeTool method="addAtomTypesId"   xpath="${molAngs}"/>
-    <xpathVisitor method="copyChild"       xpath="${molAngTop}" 
-            from="${parmAngTop}/semf:functionalForm" />
-    <xpathVisitor method="copyChild"       xpath="${molAngs}/cml:property" join="../@cmlx:atomTypesId"
-            from="${parmAngTop}" using="./cml:list[@cmlx:atomTypesId='${join.value}']" />
-    <xpathVisitor method="deleteNodes"     xpath="${molAngs}/cml:property/cml:list/cml:atomType" />
-
-    <writer xpath="${mol}" file="${out}/initialAngles.xml" /> 
- -->            
-<!-- =========== copy parameters to torsions and tidy ============== -->
-<!-- 
-    <moleculeTool method="getOrCreateTorsions"    xpath="${mol}" setId="createdTorsions"/>
-    <xpathVisitor method="addChild"        xpath="${molTors}" args="${cmlProperty}"/>
-    <atomTypeTool method="addAtomTypesId"   xpath="${molTors}"/>
-    <xpathVisitor method="copyChild"       xpath="${molTorTop}" 
-            from="${parmTorTop}/semf:functionalForm" />
-    <xpathVisitor method="copyChild"       xpath="${molTors}/cml:property" join="../@cmlx:atomTypesId"
-            from="${parmTorTop}" using="./cml:list[@cmlx:atomTypesId='${join.value}']" />
-    <xpathVisitor method="deleteNodes"
-         xpath="${molTors}/cml:property/cml:list/cml:atomType" />
-            
-    <writer xpath="${mol}" file="${out}/initialTorsions.xml" /> 
--->    
-<!-- =========== copy parameters to improper torsions and tidy ============== -->
-<!-- 
-    <moleculeTool method="getOrCreateImproperTorsions"    xpath="${mol}" setId="createdImproperTorsions"/>
-    <xpathVisitor method="addChild"        xpath="${molTors}" args="${cmlProperty}"/>
-    <xpathVisitor method="copyChild"       xpath="${molTorTop}" 
-            from="${parmTorTop}/semf:functionalForm" />
-    <xpathVisitor method="copyChild"       xpath="${molTors}/cml:property" join="../@cmlx:atomTypesId"
-            from="${parmTorTop}" using="./cml:list[@cmlx:atomTypesId='${join.value}']" />
-    <xpathVisitor method="deleteNodes"
-         xpath="${molTors}/cml:property/cml:list/cml:atomType" />
-            
-    <writer xpath="${mol}" file="${out}/initialTorsions.xml" /> 
- -->    
-<!-- =========== copy parameters to non-bonded and tidy ============== -->
-<!-- 
-    <xpathVisitor method="copyChild"        xpath="${molNonBondTop}" 
-            from="${parmNonBond}/semf:functionalForm" />
-    <atomTypeTool method="addAtomTypes"           xpath="${molNonBondTop}/cml:length"/>
-    <xpathVisitor method="copyChild"        xpath="${molNonBonds}" join="./cml:atomType[1]"
-            from="${parmNonBond}" using="./cml:list[cml:atomType[.='${join.value}']]" />
-    <xpathVisitor method="copyChild"        xpath="${molNonBonds}" join="./cml:atomType[2]"
-            from="${parmNonBond}" using="./cml:list[cml:atomType[.='${join.value}']]" />
-    <xpathVisitor method="deleteNodes" xpath="${parm}/*"/>
-    <writer xpath="/*" file="${out}/all.xml" /> 
-    <writer xpath="${mol}" file="${out}/initialNonBonded.xml" /> 
- -->
-    
-<!-- =========== 1-4 interactions ============== -->
- <!-- 
-    <moleculeTool method="getOrCreate14Lengths"    xpath="${mol}" setId="14NonBonded"/>
-    <moleculeTool method="getOrCreate14Lengths"    xpath="${mol}" setId="14Electrostatic"/>
- -->
- <!-- =========== nonbonded interactions ============== -->
-<!--  
-    <moleculeTool method="getOrCreateNonBonded"   xpath="${mol}" setId="nonBonded"/>
-    <moleculeTool method="getOrCreateNonBonded"   xpath="${mol}" setId="electrostratic"/>
- -->    
-
-
-    <energyVisitor xpath="${mol}" xpath1=".//semf:functionalForm" method="singlePoint" />
-    
-    <writer xpath="/*" file="${out}/output.cml" /> 
-
-</computation>

File src/main/resources/cml/examples/amberNew.xml

-<computation xmlns="http://www.xml-cml.org/semanticcomputation"
-    xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:cml="http://www.xml-cml.org/schema"
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-    <visitor class="org.xmlcml.semantic.visitors.HREFVisitor"/>
-    <visitor class="org.xmlcml.cml.chemistry.SemanticChemistryClasses"/>
-    <visitor class="org.xmlcml.cml.chemistry.CMLClassDecorator"/>
-
-    <queryNS prefix="semc" uri="http://www.xml-cml.org/semanticcomputation"/>
-    <queryNS prefix="semf" uri="http://www.xml-cml.org/semanticforcefields"/>
-    <queryNS prefix="cml" uri="http://www.xml-cml.org/schema"/>
-    <queryNS prefix="m" uri="http://www.w3.org/1998/Math/MathML"/>
-	<queryNS prefix="amber" uri="http://www.xml-cml.org/dict/amber:gaffType" />
-	<queryNS prefix="cmlx" uri="http://www.xml-cml.org/schema/cmlx" />
-
-     <keyValue name="a" value="AAA"/>
-     <keyValue name="b" value="this${a}and${a}"/>
-     <keyValue name="forcefield" value="src/test/resources/org/xmlcml/cml/forcefield"/>
-     <cml:molecule id="molecule" href="src/test/resources/org/xmlcml/cml/forcefield/aceticStart.cml" />
-     <!-- fails as href is not resolved
-     <cml:molecule id="molecule" href="${forcefield}/aceticStart.cml" />
-     -->
-     <!-- 
-     <geometryVisitor xpath="//cml:molecule[@id='molecule']//cml:atom" method="randomShift" shift="0.3"/>
-     -->
-     <writer xpath="//cml:molecule" file="output/random.cml"/>
-<!--      <cml:molecule id="molecule" href="src/test/resources/org/xmlcml/cml/forcefield/aceticDistorted.xml" /> -->
-    <!--  molecule must have atomTypes -->
-    <assert count="0"
-        xpath="//cml:molecule[@id='molecule']/cml:atomArray/cml:atom[not(cml:atomType[@dictRef='amber:parm94Type'])]"/>
-    
-    <cml:list id="parm94Test" href="src/main/resources/org/xmlcml/cml/forcefield/amber/parm94test.xml"/>
-<!--  add hash based on atomType children -->
-    <atomTypeTool method="addAtomTypesId" using="./cml:atomType"
-        xpath="//cml:list[@id='parm94Test']/cml:list/cml:list[count(cml:atomType)>0]" />
-    
-    <unitsVisitor xpath="//cml:list[@id='parm94Test']//cml:scalar[@dictRef='ff:angeq' or @dictRef='ff:phase']" method="degrees2Radians"/>
-    
-    <writer xpath="//cml:list[@id='parm94Test']" file="output/parm94testNew.xml" /> 
-
-<!-- === create/ensure bonds, angles, torsions, nonbonded and then hash atom types === -->
-    <moleculeTool method="getOrCreateBonds"
-        xpath="//cml:molecule[@id='molecule']" setId="createdBonds"/>
-    <moleculeTool method="getOrCreateBondOrders"
-        xpath="//cml:molecule[@id='molecule']" />
-    <moleculeTool method="getOrCreateAngles"
-        xpath="//cml:molecule[@id='molecule']"  setId="createdAngles"/>
-    <moleculeTool method="getOrCreateTorsions"
-        xpath="//cml:molecule[@id='molecule']" setId="createdTorsions"/>
-    <moleculeTool method="getOrCreateNonBonded"
-        xpath="//cml:molecule[@id='molecule']" setId="createdNonBonded"/>
-    <atomTypeTool method="addAtomTypesId"
-        xpath="//cml:molecule[@id='molecule']//cml:*[self::cml:bond | self::cml:angle | self::cml:torsion]"/>
-    <atomTypeTool method="addAtomTypes"
-        xpath="//cml:molecule[@id='molecule']/cml:list[@id='createdNonBonded']/cml:length"/>
-
-    <writer xpath="//cml:molecule[@id='molecule']" file="output/testAtomTypes0.xml" /> 
-    
-<!-- =========== copy parameters to bonds and tidy ============== -->
-    <xpathVisitor method="addChild"
-        xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond" args="org.xmlcml.cml.element.CMLProperty"/>
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:bondArray" 
-            from="//cml:list[@id='parm94Test']/cml:list[@title='bonds']/semf:functionalForm" />
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond/cml:property" key="../@cmlx:atomTypesId"
-            from="//cml:list[@id='parm94Test']/cml:list[@title='bonds']" using="./cml:list[@cmlx:atomTypesId='$key']" />
-    <xpathVisitor method="deleteNodes"
-         xpath="//cml:molecule[@id='molecule']/cml:bondArray/cml:bond/cml:property/cml:list/cml:atomType" />
-         
-<!-- =========== copy parameters to angles and tidy ============== -->
-    <xpathVisitor method="addChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list/cml:angle" args="org.xmlcml.cml.element.CMLProperty"/>
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list[cml:angle]" 
-            from="//cml:list[@id='parm94Test']/cml:list[@dictRef='ff:angles']/semf:functionalForm" />
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list/cml:angle/cml:property" key="../@cmlx:atomTypesId"
-            from="//cml:list[@id='parm94Test']/cml:list[@title='angles']" using="./cml:list[@cmlx:atomTypesId='$key']" />
-    <xpathVisitor method="deleteNodes"
-         xpath="//cml:molecule[@id='molecule']/cml:list/cml:angle/cml:property/cml:list/cml:atomType" />
-            
-<!-- =========== copy parameters to torsions and tidy ============== -->
-    <xpathVisitor method="addChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list/cml:torsion" args="org.xmlcml.cml.element.CMLProperty"/>
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list[cml:torsion]" 
-            from="//cml:list[@id='parm94Test']/cml:list[@dictRef='ff:torsions']/semf:functionalForm" />
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list/cml:torsion/cml:property" key="../@cmlx:atomTypesId"
-            from="//cml:list[@id='parm94Test']/cml:list[@title='torsions']" using="./cml:list[@cmlx:atomTypesId='$key']" />
-    <xpathVisitor method="deleteNodes"
-         xpath="//cml:molecule[@id='molecule']/cml:list/cml:torsion/cml:property/cml:list/cml:atomType" />
-            
-    <writer xpath="//cml:molecule[@id='molecule']" file="output/testAtomTypes.xml" /> 
-    
-<!-- =========== copy parameters to non-bonded and tidy ============== -->
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list[@id='createdNonBonded']" 
-            from="//cml:list[@id='parm94Test']/cml:list[@dictRef='amber:mod_re']/semf:functionalForm" />
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list[@id='createdNonBonded']/cml:length" key="./cml:atomType[1]"
-            from="//cml:list[@id='parm94Test']/cml:list[@dictRef='amber:mod_re']" using="./cml:list[cml:atomType[.='$key']]" />
-    <xpathVisitor method="copyChild"
-        xpath="//cml:molecule[@id='molecule']/cml:list[@id='createdNonBonded']/cml:length" key="./cml:atomType[2]"
-            from="//cml:list[@id='parm94Test']/cml:list[@dictRef='amber:mod_re']" using="./cml:list[cml:atomType[.='$key']]" />
-    <xpathVisitor method="deleteNodes"
-         xpath="//cml:molecule[@id='molecule']/cml:list/cml:torsion/cml:property/cml:list/cml:atomType" />
-    <xpathVisitor method="deleteNodes" xpath="//cml:list[@id='parm94Test']/*"/>
-    <writer xpath="/*" file="output/all.xml" /> 
-
-    <writer xpath="/*" file="output/allxx.xml" /> 
-
-<!--     
-    <energyVisitor xpath="//cml:molecule" xpath1=".//semf:functionalForm" method="singlePoint" />
-    -->
-     <energyVisitor xpath="//cml:molecule" xpath1=".//semf:functionalForm" method="optimise" />
-    
-    <writer xpath="/*" file="output/output.cml" /> 
-
-</computation>

File src/main/resources/cml/examples/karplusComputation.xml

-<computation xmlns="http://www.xml-cml.org/semanticcomputation"
-    xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:cml="http://www.xml-cml.org/schema"
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-	<visitorList>
-	    <visitor class="org.xmlcml.semantic.visitors.KeyValueVisitor" xpath="//*[local-name()='keyValue']"/>
-	    <visitor class="org.xmlcml.semantic.visitors.HREFVisitor"/>
-    </visitorList>
-    <visitorList>
-	    <visitor class="org.xmlcml.cml.chemistry.SemanticChemistryClasses"/>
-	    <visitor class="org.xmlcml.cml.chemistry.CMLClassDecorator"/>
-	</visitorList>
-    
-	<queryNSList>
-	    <queryNS prefix="semc"  uri="http://www.xml-cml.org/semanticcomputation"/>
-	    <queryNS prefix="semf"  uri="http://www.xml-cml.org/semanticforcefields"/>
-	    <queryNS prefix="cml"   uri="http://www.xml-cml.org/schema"/>
-	    <queryNS prefix="m"     uri="http://www.w3.org/1998/Math/MathML"/>
-		<queryNS prefix="amber" uri="http://www.xml-cml.org/dict/amber:gaffType" />
-		<queryNS prefix="cmlx"  uri="http://www.xml-cml.org/schema/cmlx" />
-	</queryNSList>
-
-	<keyValueList>
-	     <keyValue key="all"           value="/*" />
-	     <keyValue key="main"          value="src/main/resources" />
-	     <keyValue key="mainCml"       value="${main}/org/xmlcml/cml" />
-	     <keyValue key="test"          value="src/test/resources" />
-	     <keyValue key="molDir"        value="${test}/molecules" />
-	     <keyValue key="out"           value="output" />
-	     <keyValue key="mol"           value="//cml:molecule[@id='karplus1']" />
-	</keyValueList>
-
-	     <writer xpath="${all}" file="${out}/karplusStart0.cml"/>
-	     <cml:molecule id="mol" href="${molDir}/ClCCF.cml" />
-	     <moleculeTool method="getOrCreateTorsions"  xpath="${mol}" setId="createdTorsions"/>
-	     
-	     <writer xpath="${all}" file="${out}/karplusStart.cml"/>
-	     
-	    <cml:list id="karplusEquation" href="${mainCml}/karplus/bb.xml"/>
-	    
-	    <writer xpath="karplusEquation" file="${out}/karplusNew.xml" /> 
-	
-	
-	
-	<!-- === create/ensure bonds, angles, torsions, nonbonded and then hash atom types === -->
-	
-	    <writer xpath="${mol}" file="${out}/initialTemplate.xml" /> 
-	    
-	
-	    <calculationVisitor xpath="${mol}" xpath1=".//semf:functionalForm" method="singlePoint" />
-	    
-	    <writer xpath="/*" file="${out}/output.cml" /> 
-
-</computation>

File src/main/resources/cml/examples/kiharaKoba1.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<computation xmlns="http://www.xml-cml.org/semanticcomputation"
-    xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:cml="http://www.xml-cml.org/schema"
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-    <visitor class="org.xmlcml.semantic.visitors.HREFVisitor"/>
-    <visitor class="org.xmlcml.cml.chemistry.SemanticChemistryClasses"/>
-    <visitor class="org.xmlcml.cml.chemistry.CMLClassDecorator"/>
-    
-    <queryNS prefix="semc"  uri="http://www.xml-cml.org/semanticcomputation"/>
-    <queryNS prefix="semf"  uri="http://www.xml-cml.org/semanticforcefields"/>
-    <queryNS prefix="cml"   uri="http://www.xml-cml.org/schema"/>
-    <queryNS prefix="m"     uri="http://www.w3.org/1998/Math/MathML"/>
-	<queryNS prefix="amber" uri="http://www.xml-cml.org/dict/amber:gaffType" />
-	<queryNS prefix="cmlx"  uri="http://www.xml-cml.org/schema/cmlx" />
-
-	<keyValueList>
-		<keyValue key="topDir" value="src/test/resources/org/xmlcml/semantic" />
-		<keyValue key="keyvalDir" value="${topDir}/keyValue" />
-		<keyValue key="hrefDir" value="${topDir}/href" />
-		<keyValue key="doc1" value="${keyvalDir}/doc1.xml" />
-		<keyValue key="doc2" value="${keyvalDir}/doc2.xml" />
-	</keyValueList>
-	
-	<list >
-	  <array id="kk1" dataType="xsd:double" units="units:dimensionless" dictRef="ff:kkshell" count="10">1 2 3 4 5 6 7 8 9 10</array>
-	  <array id="kk2" dataType="xsd:double" units="units:dimensionless" dictRef="ff:kknci" count="10">12 6 24 12 24 8 48 6 36 24</array>
-	</list >
-
-    <mathml href="sumDoubles" setId="mathSum"/>	
-	<calculation xpath=".//cml:array[@id='kk2']" mathml="sumDoubles" 
-</computation>

File src/main/resources/cml/forcefield/amber/AMBERFF.mml

-<!-- Content MathML of the AMBER FF -->
-
-<math display = 'block'>
-
-<!-- Content MathML for Bonded terms in AMBER -->
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>bond</ci>
-        <ci type='set'>bonds</ci>
-      </apply>
-    </condition>
-    <apply>
-      <times/>
-      <ci>k</ci>
-      <apply>
-        <power/>
-        <apply>
-          <minus/>
-          <apply>
-            <csymbol>bondlength</csymbol>
-            <ci>bond</ci>
-          </apply>
-          <ci>x0</ci>
-        </apply>
-        <cn>2</cn>
-      </apply>
-    </apply>
-  </apply>
-
-
-
-<!-- Content MathML for angle term in AMBER -->
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>angle</ci>
-        <ci type='set'>angles</ci>
-      </apply>
-    </condition>
-    <apply>
-      <times/>
-      <ci>k</ci>
-      <apply>
-        <power/>
-        <apply>
-          <minus/>
-          <apply>
-            <csymbol>anglesize</csymbol>
-            <ci>angle</ci>
-          </apply>
-          <ci>theta0</ci>
-        </apply>
-        <cn>2</cn>
-      </apply>
-    </apply>
-  </apply>
-
-
-
-<!-- Content MathML for Dihedral terms in AMBER -->
-
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>torsion</ci>
-        <ci type='set'>torsions</ci>
-      </apply>
-    </condition>
-
-    <apply>
-      <times/>
-      <cn>0.5</cn>
-      <apply>
-        <times/>
-        <ci>Vn</ci>
-        <apply>
-          <plus/>
-          <apply>
-            <cos/>
-            <apply>
-              <times/>
-              <ci>n</ci>
-              <apply>
-                <minus/>
-                <apply>
-                  <csymbol>torisonangle</csymbol>
-                  <ci>torsion</ci>
-                </apply>
-                <ci>phase</ci>
-              </apply>
-            </apply>
-          </apply>
-          <cn>1</cn>
-        </apply>
-      </apply>
-    </apply>
-  </apply>
-
-
-
-
-<!-- Content MathML for Vdw terms in AMBER -->
-
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>pair</ci>
-        <ci type='set'>pairs</ci>
-      </apply>
-    </condition>
-    <apply>
-      <times/>
-      <apply>
-        <minus/>
-        <apply>
-          <power/>
-          <apply>
-            <divide/>
-            <ci>r0ij</ci>
-            <apply>
-              <csymbol>distance</csymbol>
-              <ci>pair</ci>
-            </apply>
-          </apply>
-          <cn>12</cn>
-        </apply>
-        <apply>
-          <times/>
-          <cn>2</cn>
-          <apply>
-            <power/>
-            <apply>
-              <divide/>
-              <ci>r0ij</ci>
-              <apply>
-                <csymbol>distance</csymbol>
-                <ci>pair</ci>
-              </apply>
-            </apply>
-            <cn>6</cn>
-          </apply>
-        </apply>
-      </apply>
-      <ci>epsilonij</ci>
-    </apply>
-  </apply>
-
-
-
-
-<!-- Content MathML for 14Vdw terms in AMBER  -->
-
-
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>pair</ci>
-        <ci type='set'>14pairs</ci>
-      </apply>
-    </condition>
-    <apply>
-      <times/>
-      <ci>SCNB</ci>
-      <apply>
-        <times/>
-        <apply>
-          <minus/>
-          <apply>
-            <power/>
-            <apply>
-              <divide/>
-              <ci>r0ij</ci>
-              <apply>
-                <csymbol>distance</csymbol>
-                <ci>pair</ci>
-              </apply>
-            </apply>
-            <cn>12</cn>
-          </apply>
-          <apply>
-            <times/>
-            <cn>2</cn>
-            <apply>
-              <power/>
-              <apply>
-                <divide/>
-                <ci>r0ij</ci>
-                <apply>
-                  <csymbol>distance</csymbol>
-                  <ci>pair</ci>
-                </apply>
-              </apply>
-              <cn>6</cn>
-            </apply>
-          </apply>
-        </apply>
-        <ci>epsilonij</ci>
-      </apply>
-    </apply>
-  </apply>
-
-
-
-
-
-
-<!-- Content MathML for ee terms in AMBER -->
-
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>pair</ci>
-        <ci type='set'>pairs</ci>
-      </apply>
-    </condition>
-    <apply>
-      <divide/>
-      <apply>
-        <times/>
-        <ci>qi</ci>
-        <ci>qj</ci>
-      </apply>
-      <apply>
-        <times/>
-        <apply>
-          <times/>
-          <apply>
-            <times/>
-            <cn>4</cn>
-            <ci>epsilon</ci>
-          </apply>
-          <ci>pi</ci>
-        </apply>
-        <apply>
-          <csymbol>distance</csymbol>
-          <ci>pair</ci>
-        </apply>
-      </apply>
-    </apply>
-  </apply>
-
-
-
-
-
-
-<!-- Content MathML for 14ee terms in AMBER -->
-
-  <apply>
-    <sum/>
-    <bvar>
-      <ci>x</ci>
-    </bvar>
-    <condition>
-      <apply>
-        <in/>
-        <ci>pair</ci>
-        <ci type='set'>14pairs</ci>
-      </apply>
-    </condition>
-    <apply>
-      <times/>
-      <ci>SCEE</ci>
-      <apply>
-        <divide/>
-        <apply>
-          <times/>
-          <ci>qi</ci>
-          <ci>qj</ci>
-        </apply>
-        <apply>
-          <times/>
-          <apply>
-            <times/>
-            <apply>
-              <times/>
-              <cn>4</cn>
-              <ci>epsilon</ci>
-            </apply>
-            <ci>pi</ci>
-          </apply>
-          <apply>
-            <csymbol>distance</csymbol>
-            <ci>pair</ci>
-          </apply>
-        </apply>
-      </apply>
-    </apply>
-  </apply>
-</math>

File src/main/resources/cml/forcefield/amber/gaffmini.xml

-<cml:list xmlns:cml='http://www.xml-cml.org/schema' title='amberforcefield gaff'
-	id='gaff' xmlns:gaff='http://www.xmlcml.org/dict/amber/gaff'
-	convention='convention:forcefield' xmlns:convention='http://www.xml-cml.org/convention/'>
-	<!-- limited selection of types -->
-	<cml:list title="harmonic bonds">
-		<cml:list title="c3-hc">
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>hc</cml:atomType>
-			<cml:scalar dataType="xsd:double" dictRef='ff:kijharmconst'
-				id='kij_c3_hc' units='units:kg-ang-2-mol-1'>337.3</cml:scalar>
-			<cml:scalar dataType="xsd:double" dictRef='ff:rijeqdist'
-				role="dist" id='rij_c3_hc' units='units:ang'>1.092</cml:scalar>
-		</cml:list>
-		<cml:list title="oh-ho">
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>ho</cml:atomType>
-			<cml:scalar dataType="xsd:double" dictRef='ff:kijharmconst'
-				id='kij_oh_ho' units='units:kg-ang-2-mol-1'>369.6</cml:scalar>
-			<cml:scalar dataType="xsd:double" dictRef='ff:rijeqdist'
-				role="dist" id='rij_oh_ho' units='units:ang'>0.974</cml:scalar>
-		</cml:list>
-		<cml:list title="c3-c">
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:scalar dataType="xsd:double" dictRef='ff:kijharmconst'
-				id='kij_c3_c' units='units:kg-ang-2-mol-1'>328.3</cml:scalar>
-			<cml:scalar dataType="xsd:double" dictRef='ff:rijeqdist'
-				role="dist" id='rij_c3_c' units='units:ang'>1.508</cml:scalar>
-		</cml:list>
-		<cml:list title="c-o">
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:scalar dataType="xsd:double" dictRef='ff:kijharmconst'
-				id='kij_c_o' units='units:kg-ang-2-mol-1'>648.0</cml:scalar>
-			<cml:scalar dataType="xsd:double" dictRef='ff:rijeqdist'
-				role="dist" id='rij_c_o' units='units:ang'>1.214</cml:scalar>
-		</cml:list>
-		<cml:list title="c-oh">
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:scalar dataType="xsd:double" dictRef='ff:kijharmconst'
-				id='kij_c_oh' units='units:kg-ang-2-mol-1'>466.4</cml:scalar>
-			<cml:scalar dataType="xsd:double" dictRef='ff:rijeqdist'
-				role="dist" id='rij_c_oh' units='units:ang'>1.306</cml:scalar>
-		</cml:list>
-	</cml:list>
-
-	<cml:list title="angles">
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>hc</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>47.200</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_c_c3_hc' units='units:degrees'>109.680</cml:scalar>
-		</cml:list>
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>ho</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>51.190</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_c_oh_ho'
-				units='units:degrees'>107.370</cml:scalar>
-		</cml:list>
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>hc</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>hc</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>39.430</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_hc_c3_hc'
-				units='units:degrees'>108.350</cml:scalar>
-		</cml:list>
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>68.030</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_c3_c_o'
-				units='units:degrees'>123.110</cml:scalar>
-		</cml:list>
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>69.840</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_c3_c_oh'
-				units='units:degrees'>112.200</cml:scalar>
-		</cml:list>
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:scalar dictRef='ff:aijkharmconst' units='units:kcal-mol-1-rad-2'>77.380</cml:scalar>
-			<cml:scalar dictRef='ff:aijkangeq' role='ang' id='aijk_o_c_oh'
-				units='units:degrees'>122.880</cml:scalar>
-		</cml:list>
-	</cml:list>
-
-	<cml:list title="torsions">
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>ho</cml:atomType>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>2</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>4.600</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>180.000</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>2.000</cml:scalar>
-			</cml:list>
-		</cml:list>
-
-
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>hc</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>1</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>0.80</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>0.0</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>1.</cml:scalar>
-			</cml:list>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>1</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>0.08</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>180.0</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>3.</cml:scalar>
-			</cml:list>
-		</cml:list>
-
-
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>ho</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>1</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>2.30</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>180.0</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>-2.</cml:scalar>
-			</cml:list>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>1</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>1.90</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>0.0</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>1.</cml:scalar>
-			</cml:list>
-		</cml:list>
-
-		<cml:list>
-			<cml:atomType dictRef='amber:gaffType'>c3</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>o</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>c</cml:atomType>
-			<cml:atomType dictRef='amber:gaffType'>oh</cml:atomType>
-			<cml:list>
-				<cml:scalar dictRef='ff:idivf' units='units:kcal-mol-1-rad-2'>1</cml:scalar>
-				<cml:scalar dictRef='ff:pk' units='units:kcal-mol-1-rad-2'>1.1</cml:scalar>
-				<cml:scalar dictRef='ff:phase' units='units:kcal-mol-1-rad-2'>180.</cml:scalar>
-				<cml:scalar dictRef='ff:pn' units='units:kcal-mol-1-rad-2'>2.</cml:scalar>
-			</cml:list>
-		</cml:list>
-	</cml:list>
-	<!-- where: IDIVF The factor by which the torsional barrier is divided. 
-		Consult Weiner, et al., JACS 106:765 (1984) p. 769 for details. Basically, 
-		the actual torsional potential is (PK/IDIVF) * (1 + cos(PN*phi - PHASE)) 
-		PK The barrier height divided by a factor of 2. PHASE The phase shift angle 
-		in the torsional function. The unit is degrees. PN The periodicity of the 
-		torsional barrier. NOTE: If PN .lt. 0.0 then the torsional potential is assumed 
-		to have more than one term, and the values of the rest of the terms are read 
-		from the next cards until a positive PN is encountered. The negative value 
-		of pn is used only for identifying the existence of the next term and only 
-		the absolute value of PN is kept. Note for more information about dihedrals, 
-		please see page 254 of http://ambermd.org/doc8/amber8.pdf -->
-
-	<!-- VDW === R EDEP hc 1.4870 0.0157 c3 1.9080 0.1094 c 1.9080 0.0860 o 
-		1.6612 0.2100 oh 1.7210 0.2104 ho 0.0000 0.0000 -->
-	<!-- van der Waals Parameters in Amber There are two common formulations 
-		of the van der Waals equation: EVDW=4[ r 12 − r 6] and EVDW=4[1 4 
-		r0 r 12 −1 2 r0 r 6] Both describe the nonbonded interaction between 
-		two particles at distance r as the sum of an attractive r6 and a repulsive 
-		r12 term. Two parameters are needed, the well depth  and a characteristic 
-		distance r0 or  (the two formulations are identical for r0=62 ). In the 
-		Amber forcefield, the later format is used, because of the easy physical 
-		interpretation of r0 as the energetically most favorable distance of two 
-		atoms. In the parameter files, every atom type is given a radius and well 
-		depth parameter, e.g. OH 1.7210 0.2104 CT 1.9080 0.1094 where the first number 
-		is the atomic radius in Angstrom and the second the well depth in kcal/mol. 
-		These values are then (at the time a prmtop file is written) combined to 
-		provide parameters for all pairs of atom types in the system: rij=rir j 
-		and ij=i j These atom pair parameters are then used to calculate the 
-		ACOEFF and BCOEFF values in the prmtop file: ACOEFF=r0 12 ; BCOEFF=2 r0 
-		6 E.g. for OH-CT nonbonded contacts, this gives: ACOEFF = 7.91544157E+05 
-		BCOEFF = 6.93079947E+02 The A and B coefficients are then used in sander's 
-		internal version of the VDW equation: EVDW= ACOEFF r/ ˚A12 − BCOEFF r 
-		/ ˚A6 Thomas Steinbrecher, TSRI 2008 (steinbrt@scripps.edu) -->
-</cml:list> 
-

File src/main/resources/cml/forcefield/amber/parm94.dat

-PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
-2	BR 79.90                !            bromine
-3	C  12.01                             sp2 C carbonyl group
-4	CA 12.01                             sp2 C pure aromatic (benzene)
-5	CB 12.01                             sp2 aromatic C, 5&6 membered ring junction
-6	CC 12.01                             sp2 aromatic C, 5 memb. ring HIS
-7	CK 12.01                             sp2 C 5 memb.ring in purines
-8	CM 12.01                             sp2 C  pyrimidines in pos. 5 & 6
-9	CN 12.01                             sp2 C aromatic 5&6 memb.ring junct.(TRP)
-10	CQ 12.01                             sp2 C in 5 mem.ring of purines between 2 N
-11	CR 12.01                             sp2 arom as CQ but in HIS
-12	CT 12.01                             sp3 aliphatic C
-13	CV 12.01                             sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
-14	CW 12.01                             sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
-15	C* 12.01                             sp2 arom. 5 memb.ring w/1 subst. (TRP)
-16	C0 40.08                             calcium
-17	F  19.00                             fluorine
-18	H  1.008                             H bonded to nitrogen atoms
-19	HC 1.008                             H aliph. bond. to C without electrwd.group
-20	H1 1.008                             H aliph. bond. to C with 1 electrwd. group
-21	H2 1.008                             H aliph. bond. to C with 2 electrwd.groups
-22	H3 1.008                             H aliph. bond. to C with 3 eletrwd.groups
-23	HA 1.008                             H arom. bond. to C without elctrwd. groups
-24	H4 1.008                             H arom. bond. to C with 1 electrwd. group
-25	H5 1.008                             H arom. bond. to C with 2 electrwd. groups
-26	HO 1.008                             hydroxyl group
-27	HS 1.008                             hydrogen bonded to sulphur
-28	HW 1.008                             H in TIP3P water
-29	HP 1.008                             H bonded to C next to positively charged gr
-30	I  126.9                             iodine
-31	IM 35.45                             assumed to be Cl-
-32	IP 22.99                             assumed to be Na+
-33	IB 131.0                             'big ion w/ waters' for vacuum (Na+, 6H2O)
-34	MG 24.305                            magnesium
-35	N  14.01                             sp2 nitrogen in amide groups
-36	NA 14.01                             sp2 N in 5 memb.ring w/H atom (HIS)
-37	NB 14.01                             sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
-38	NC 14.01                             sp2 N in 6 memb.ring w/LP (ADE,GUA)
-39	N2 14.01                             sp2 N in amino groups
-40	N3 14.01                             sp3 N for charged amino groups (Lys, etc)
-41	N* 14.01                             sp2 N
-42	O  16.00                             carbonyl group oxygen
-43	OW 16.00                             oxygen in TIP3P water
-44	OH 16.00                             oxygen in hydroxyl group
-45	OS 16.00                             ether and ester oxygen
-46	O2 16.00                             carboxyl and phosphate group oxygen
-47	P  30.97                             phosphate
-48	S  32.06                             sulphur in disulfide linkage
-49	SH 32.06                             sulphur in cystine
-50	CU 63.55                             copper
-51	FE 55.00                             iron
-52	Li  6.94                             lithium
-53	K  39.10                             potassium
-54	Rb 85.47                             rubidium
-55	Cs 132.91                            cesium
-56	
-57	C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2
-58	OW-HW  553.0    0.9572    ! TIP3P water
-59	HW-HW  553.0    1.5136      TIP3P water
-60	C -CA  469.0    1.409       JCC,7,(1986),230; TYR
-61	C -CB  447.0    1.419       JCC,7,(1986),230; GUA
-62	C -CM  410.0    1.444       JCC,7,(1986),230; THY,URA
-63	C -CT  317.0    1.522       JCC,7,(1986),230; AA
-64	C -N*  424.0    1.383       JCC,7,(1986),230; CYT,URA
-65	C -NA  418.0    1.388       JCC,7,(1986),230; GUA.URA
-66	C -NC  457.0    1.358       JCC,7,(1986),230; CYT
-67	C -O   570.0    1.229       JCC,7,(1986),230; AA,CYT,GUA,THY,URA
-68	C -O2  656.0    1.250       JCC,7,(1986),230; GLU,ASP
-69	C -OH  450.0    1.364       JCC,7,(1986),230; TYR
-70	CA-CA  469.0    1.400       JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
-71	CA-CB  469.0    1.404       JCC,7,(1986),230; ADE,TRP
-72	CA-CM  427.0    1.433       JCC,7,(1986),230; CYT
-73	CA-CT  317.0    1.510       JCC,7,(1986),230; PHE,TYR
-74	CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
-75	CA-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; no assigned
-76	CA-N2  481.0    1.340       JCC,7,(1986),230; ARG,CYT,GUA
-77	CA-NA  427.0    1.381       JCC,7,(1986),230; GUA
-78	CA-NC  483.0    1.339       JCC,7,(1986),230; ADE,CYT,GUA
-79	CB-CB  520.0    1.370       JCC,7,(1986),230; ADE,GUA
-80	CB-N*  436.0    1.374       JCC,7,(1986),230; ADE,GUA
-81	CB-NB  414.0    1.391       JCC,7,(1986),230; ADE,GUA
-82	CB-NC  461.0    1.354       JCC,7,(1986),230; ADE,GUA
-83	CK-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
-84	CK-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
-85	CK-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
-86	CM-CM  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
-87	CM-CT  317.0    1.510       JCC,7,(1986),230; THY
-88	CM-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
-89	CM-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
-90	CM-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; not assigned
-91	CM-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
-92	CQ-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE
-93	CQ-NC  502.0    1.324       JCC,7,(1986),230; ADE
-94	CT-CT  310.0    1.526       JCC,7,(1986),230; AA, SUGARS
-95	CT-HC  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, SUGARS
-96	CT-H1  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE
-97	CT-H2  340.0    1.090       changed from 331 bsd on NMA nmodes; SUGARS
-98	CT-H3  340.0    1.090       changed from 331 bsd on NMA nmodes; not assigned
-99	CT-HP  340.0    1.090        changed from 331; AA-lysine, methyl ammonium cation
-100	CT-N*  337.0    1.475       JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
-101	CT-N2  337.0    1.463       JCC,7,(1986),230; ARG
-102	CT-OH  320.0    1.410       JCC,7,(1986),230; SUGARS
-103	CT-OS  320.0    1.410       JCC,7,(1986),230; NUCLEIC ACIDS
-104	H -N2  434.0    1.010       JCC,7,(1986),230; ADE,CYT,GUA,ARG
-105	H -N*  434.0    1.010       for plain unmethylated bases ADE,CYT,GUA,ARG
-106	H -NA  434.0    1.010       JCC,7,(1986),230; GUA,URA,HIS
-107	HO-OH  553.0    0.960       JCC,7,(1986),230; SUGARS,SER,TYR
-108	HO-OS  553.0    0.960       JCC,7,(1986),230; NUCLEOTIDE ENDS
-109	O2-P   525.0    1.480       JCC,7,(1986),230; NA PHOSPHATES
-110	OH-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
-111	OS-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
-112	C*-HC  367.0    1.080       changed from 340. bsd on C6H6 nmodes, not needed AA
-113	C -N   490.0    1.335       JCC,7,(1986),230; AA
-114	C*-CB  388.0    1.459       JCC,7,(1986),230; TRP
-115	C*-CT  317.0    1.495       JCC,7,(1986),230; TRP
-116	C*-CW  546.0    1.352       JCC,7,(1986),230; TRP
-117	CA-CN  469.0    1.400       JCC,7,(1986),230; TRP
-118	CB-CN  447.0    1.419       JCC,7,(1986),230; TRP
-119	CC-CT  317.0    1.504       JCC,7,(1986),230; HIS
-120	CC-CV  512.0    1.375       JCC,7,(1986),230; HIS(delta)
-121	CC-CW  518.0    1.371       JCC,7,(1986),230; HIS(epsilon)
-122	CC-NA  422.0    1.385       JCC,7,(1986),230; HIS
-123	CC-NB  410.0    1.394       JCC,7,(1986),230; HIS
-124	CN-NA  428.0    1.380       JCC,7,(1986),230; TRP
-125	CR-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS
-126	CR-NA  477.0    1.343       JCC,7,(1986),230; HIS
-127	CR-NB  488.0    1.335       JCC,7,(1986),230; HIS
-128	CT-N   337.0    1.449       JCC,7,(1986),230; AA
-129	CT-N3  367.0    1.471       JCC,7,(1986),230; LYS
-130	CT-S   227.0    1.810       changed from 222.0 based on dimethylS nmodes
-131	CT-SH  237.0    1.810       changed from 222.0 based on methanethiol nmodes
-132	CV-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; HIS
-133	CV-NB  410.0    1.394       JCC,7,(1986),230; HIS
-134	CW-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
-135	CW-NA  427.0    1.381       JCC,7,(1986),230; HIS,TRP
-136	H -N   434.0    1.010       JCC,7,(1986),230; AA
-137	H -N3  434.0    1.010       JCC,7,(1986),230; LYS   
-138	HS-SH  274.0    1.336       JCC,7,(1986),230; CYS
-139	S -S   166.0    2.038       JCC,7,(1986),230; CYX   (SCHERAGA)
-140	CT-F   367.0    1.380       JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
-141	
-142	HW-OW-HW    100.      104.52    TIP3P water
-143	HW-HW-OW      0.      127.74    (found in crystallographic water with 3 bonds)
-144	CB-C -NA    70.0      111.30    NA
-145	CB-C -O     80.0      128.80
-146	CM-C -NA    70.0      114.10
-147	CM-C -O     80.0      125.30
-148	CT-C -O     80.0      120.40
-149	CT-C -O2    70.0      117.00
-150	CT-C -OH    70.0      117.00
-151	N*-C -NA    70.0      115.40
-152	N*-C -NC    70.0      118.60
-153	N*-C -O     80.0      120.90
-154	NA-C -O     80.0      120.60
-155	NC-C -O     80.0      122.50
-156	CT-C -N     70.0      116.60    AA general
-157	N -C -O     80.0      122.90    AA general
-158	O -C -O     80.0      126.00    AA COO- terminal residues
-159	O2-C -O2    80.0      126.00    AA GLU            (SCH JPC 79,2379)
-160	O -C -OH    80.0      126.00
-161	CA-C -CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA tyr
-162	CA-C -OH    70.0      120.00    AA tyr
-163	C -CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
-164	CA-CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
-165	CA-CA-CB    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
-166	CA-CA-CT    70.0      120.00
-167	CA-CA-HA    35.0      120.00
-168	CA-CA-H4    35.0      120.00
-169	CB-CA-HA    35.0      120.00
-170	CB-CA-H4    35.0      120.00
-171	CB-CA-N2    70.0      123.50
-172	CB-CA-NC    70.0      117.30
-173	CM-CA-N2    70.0      120.10
-174	CM-CA-NC    70.0      121.50
-175	N2-CA-NA    70.0      116.00
-176	N2-CA-NC    70.0      119.30
-177	NA-CA-NC    70.0      123.30
-178	C -CA-HA    35.0      120.00    AA tyr
-179	N2-CA-N2    70.0      120.00    AA arg
-180	CN-CA-HA    35.0      120.00    AA trp
-181	CA-CA-CN    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA trp
-182	C -CB-CB    63.0      119.20    changed from 85.0  bsd on C6H6 nmodes; NA gua
-183	C -CB-NB    70.0      130.00
-184	CA-CB-CB    63.0      117.30    changed from 85.0  bsd on C6H6 nmodes; NA ade
-185	CA-CB-NB    70.0      132.40   
-186	CB-CB-N*    70.0      106.20
-187	CB-CB-NB    70.0      110.40
-188	CB-CB-NC    70.0      127.70
-189	N*-CB-NC    70.0      126.20
-190	C*-CB-CA    63.0      134.90    changed from 85.0  bsd on C6H6 nmodes; AA trp
-191	C*-CB-CN    63.0      108.80    changed from 85.0  bsd on C6H6 nmodes; AA trp
-192	CA-CB-CN    63.0      116.20    changed from 85.0  bsd on C6H6 nmodes; AA trp
-193	H5-CK-N*    35.0      123.05
-194	H5-CK-NB    35.0      123.05
-195	N*-CK-NB    70.0      113.90
-196	C -CM-CM    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
-197	C -CM-CT    70.0      119.70
-198	C -CM-HA    35.0      119.70
-199	C -CM-H4    35.0      119.70
-200	CA-CM-CM    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
-201	CA-CM-HA    35.0      123.30
-202	CA-CM-H4    35.0      123.30
-203	CM-CM-CT    70.0      119.70
-204	CM-CM-HA    35.0      119.70
-205	CM-CM-H4    35.0      119.70
-206	CM-CM-N*    70.0      121.20
-207	H4-CM-N*    35.0      119.10
-208	H5-CQ-NC    35.0      115.45
-209	NC-CQ-NC    70.0      129.10
-210	CM-CT-HC    50.0      109.50    changed based on NMA nmodes
-211	CT-CT-CT    40.0      109.50
-212	CT-CT-HC    50.0      109.50    changed based on NMA nmodes
-213	CT-CT-H1    50.0      109.50    changed based on NMA nmodes
-214	CT-CT-H2    50.0      109.50    changed based on NMA nmodes
-215	CT-CT-HP    50.0      109.50    changed based on NMA nmodes
-216	CT-CT-N*    50.0      109.50
-217	CT-CT-OH    50.0      109.50
-218	CT-CT-OS    50.0      109.50
-219	HC-CT-HC    35.0      109.50
-220	H1-CT-H1    35.0      109.50
-221	HP-CT-HP    35.0      109.50    AA lys, ch3nh4+
-222	H2-CT-N*    50.0      109.50    changed based on NMA nmodes
-223	H1-CT-N*    50.0      109.50    changed based on NMA nmodes
-224	H1-CT-OH    50.0      109.50    changed based on NMA nmodes
-225	H1-CT-OS    50.0      109.50    changed based on NMA nmodes
-226	H2-CT-OS    50.0      109.50    changed based on NMA nmodes
-227	N*-CT-OS    50.0      109.50
-228	H1-CT-N     50.0      109.50    AA general  changed based on NMA nmodes
-229	C -CT-H1    50.0      109.50    AA general  changed based on NMA nmodes
-230	C -CT-HP    50.0      109.50    AA zwitterion  changed based on NMA nmodes
-231	H1-CT-S     50.0      109.50    AA cys     changed based on NMA nmodes
-232	H1-CT-SH    50.0      109.50    AA cyx     changed based on NMA nmodes
-233	CT-CT-S     50.0      114.70    AA cyx            (SCHERAGA  JPC 79,1428)
-234	CT-CT-SH    50.0      108.60    AA cys
-235	H2-CT-H2    35.0      109.50    AA lys
-236	H1-CT-N2    50.0      109.50    AA arg     changed based on NMA nmodes
-237	HP-CT-N3    50.0      109.50    AA lys, ch3nh3+, changed based on NMA nmodes
-238	CA-CT-CT    63.0      114.00    AA phe tyr          (SCH JPC  79,2379)
-239	C -CT-HC    50.0      109.50    AA gln      changed based on NMA nmodes
-240	C -CT-N     63.0      110.10    AA general
-241	CT-CT-N2    80.0      111.20    AA arg             (JCP 76, 1439)
-242	CT-CT-N     80.0      109.70    AA ala, general    (JACS 94, 2657)
-243	C -CT-CT    63.0      111.10    AA general
-244	CA-CT-HC    50.0      109.50    AA tyr     changed based on NMA nmodes
-245	CT-CT-N3    80.0      111.20    AA lys             (JCP 76, 1439)
-246	CC-CT-CT    63.0      113.10    AA his
-247	CC-CT-HC    50.0      109.50    AA his     changed based on NMA nmodes
-248	C -CT-N3    80.0      111.20    AA amino terminal residues
-249	C*-CT-CT    63.0      115.60    AA trp
-250	C*-CT-HC    50.0      109.50    AA trp    changed based on NMA nmodes
-251	CT-CC-NA    70.0      120.00    AA his
-252	CT-CC-CV    70.0      120.00    AA his
-253	CT-CC-NB    70.0      120.00    AA his
-254	CV-CC-NA    70.0      120.00    AA his
-255	CW-CC-NA    70.0      120.00    AA his
-256	CW-CC-NB    70.0      120.00    AA his
-257	CT-CC-CW    70.0      120.00    AA his
-258	H5-CR-NA    35.0      120.00    AA his
-259	H5-CR-NB    35.0      120.00    AA his
-260	NA-CR-NA    70.0      120.00    AA his
-261	NA-CR-NB    70.0      120.00    AA his
-262	CC-CV-H4    35.0      120.00    AA his
-263	CC-CV-NB    70.0      120.00    AA his
-264	H4-CV-NB    35.0      120.00    AA his
-265	CC-CW-H4    35.0      120.00    AA his
-266	CC-CW-NA    70.0      120.00    AA his
-267	H4-CW-NA    35.0      120.00    AA his
-268	C*-CW-H4    35.0      120.00    AA trp
-269	C*-CW-NA    70.0      108.70    AA trp
-270	CT-C*-CW    70.0      125.00    AA trp
-271	CB-C*-CT    70.0      128.60    AA trp
-272	CB-C*-CW    63.0      106.40    changed from 85.0  bsd on C6H6 nmodes; AA trp
-273	CA-CN-NA    70.0      132.80    AA trp
-274	CB-CN-NA    70.0      104.40    AA trp
-275	CA-CN-CB    63.0      122.70    changed from 85.0  bsd on C6H6 nmodes; AA trp
-276	C -N -CT    50.0      121.90    AA general
-277	C -N -H     30.0      120.00    AA general, gln, asn,changed based on NMA nmodes
-278	CT-N -H     30.0      118.04    AA general,     changed based on NMA nmodes
-279	CT-N -CT    50.0      118.00    AA pro             (DETAR JACS 99,1232)
-280	H -N -H     35.0      120.00    ade,cyt,gua,gln,asn     **
-281	C -N*-CM    70.0      121.60
-282	C -N*-CT    70.0      117.60
-283	C -N*-H     30.0      119.20    changed based on NMA nmodes
-284	CB-N*-CK    70.0      105.40
-285	CB-N*-CT    70.0      125.80
-286	CB-N*-H     30.0      125.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
-287	CK-N*-CT    70.0      128.80
-288	CK-N*-H     30.0      128.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
-289	CM-N*-CT    70.0      121.20
-290	CM-N*-H     30.0      121.20    for unmethylated n.a. bases,chngd bsd NMA nmodes
-291	CA-N2-H     35.0      120.00   
-292	H -N2-H     35.0      120.00   
-293	CT-N2-H     35.0      118.40    AA arg
-294	CA-N2-CT    50.0      123.20    AA arg
-295	CT-N3-H     50.0      109.50    AA lys,     changed based on NMA nmodes
-296	CT-N3-CT    50.0      109.50    AA pro/nt
-297	H -N3-H     35.0      109.50    AA lys, AA(end)
-298	C -NA-C     70.0      126.40
-299	C -NA-CA    70.0      125.20
-300	C -NA-H     30.0      116.80    changed based on NMA nmodes
-301	CA-NA-H     30.0      118.00    changed based on NMA nmodes
-302	CC-NA-CR    70.0      120.00    AA his
-303	CC-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
-304	CR-NA-CW    70.0      120.00    AA his
-305	CR-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
-306	CW-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
-307	CN-NA-CW    70.0      111.60    AA trp
-308	CN-NA-H     30.0      123.10    AA trp,    changed based on NMA nmodes
-309	CB-NB-CK    70.0      103.80
-310	CC-NB-CR    70.0      117.00    AA his
-311	CR-NB-CV    70.0      117.00    AA his
-312	C -NC-CA    70.0      120.50
-313	CA-NC-CB    70.0      112.20
-314	CA-NC-CQ    70.0      118.60
-315	CB-NC-CQ    70.0      111.00
-316	C -OH-HO    35.0      113.00
-317	CT-OH-HO    55.0      108.50
-318	HO-OH-P     45.0      108.50
-319	CT-OS-CT    60.0      109.50
-320	CT-OS-P    100.0      120.50
-321	P -OS-P    100.0      120.50
-322	O2-P -OH    45.0      108.23
-323	O2-P -O2   140.0      119.90
-324	O2-P -OS   100.0      108.23
-325	OH-P -OS    45.0      102.60
-326	OS-P -OS    45.0      102.60
-327	CT-S -CT    62.0       98.90    AA met
-328	CT-S -S     68.0      103.70    AA cyx             (SCHERAGA  JPC 79,1428)
-329	CT-SH-HS    43.0       96.00    changed from 44.0 based on methanethiol nmodes
-330	HS-SH-HS    35.0       92.07    AA cys
-331	F -CT-F     77.0      109.10    JCC,13,(1992),963;
-332	F -CT-H1    35.0      109.50    JCC,13,(1992),963;
-333	
-334	X -C -CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
-335	X -C -CB-X    4   12.00        180.0             2.         intrpol.bsd.on C6H6
-336	X -C -CM-X    4    8.70        180.0             2.         intrpol.bsd.on C6H6
-337	X -C -N*-X    4    5.80        180.0             2.         JCC,7,(1986),230
-338	X -C -NA-X    4    5.40        180.0             2.         JCC,7,(1986),230
-339	X -C -NC-X    2    8.00        180.0             2.         JCC,7,(1986),230
-340	X -C -OH-X    2    1.80        180.0             2.         JCC,7,(1986),230
-341	X -C -CT-X    4    0.00          0.0             2.         JCC,7,(1986),230
-342	X -CA-CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
-343	X -CA-CB-X    4   14.00        180.0             2.         intrpol.bsd.on C6H6
-344	X -CA-CM-X    4   10.20        180.0             2.         intrpol.bsd.on C6H6
-345	X -CA-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
-346	X -CA-N2-X    4    9.60        180.0             2.         reinterpolated 93'
-347	X -CA-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
-348	X -CA-NC-X    2    9.60        180.0             2.         JCC,7,(1986),230
-349	X -CB-CB-X    4   21.80        180.0             2.         intrpol.bsd.on C6H6
-350	X -CB-N*-X    4    6.60        180.0             2.         JCC,7,(1986),230
-351	X -CB-NB-X    2    5.10        180.0             2.         JCC,7,(1986),230
-352	X -CB-NC-X    2    8.30        180.0             2.         JCC,7,(1986),230
-353	X -CK-N*-X    4    6.80        180.0             2.         JCC,7,(1986),230
-354	X -CK-NB-X    2   20.00        180.0             2.         JCC,7,(1986),230
-355	X -CM-CM-X    4   26.60        180.0             2.         intrpol.bsd.on C6H6
-356	X -CM-CT-X    6    0.00          0.0             3.         JCC,7,(1986),230
-357	X -CM-N*-X    4    7.40        180.0             2.         JCC,7,(1986),230
-358	X -CQ-NC-X    2   13.60        180.0             2.         JCC,7,(1986),230
-359	X -CT-CT-X    9    1.40          0.0             3.         JCC,7,(1986),230
-360	X -CT-N -X    6    0.00          0.0             2.         JCC,7,(1986),230
-361	X -CT-N*-X    6    0.00          0.0             2.         JCC,7,(1986),230
-362	X -CT-N2-X    6    0.00          0.0             3.         JCC,7,(1986),230
-363	X -CT-OH-X    3    0.50          0.0             3.         JCC,7,(1986),230
-364	X -CT-OS-X    3    1.15          0.0             3.         JCC,7,(1986),230
-365	X -OH-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
-366	X -OS-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
-367	X -C -N -X    4   10.00        180.0             2.         AA|check Wendy?&NMA
-368	X -CT-N3-X    9    1.40          0.0             3.         JCC,7,(1986),230
-369	X -CT-S -X    3    1.00          0.0             3.         JCC,7,(1986),230
-370	X -CT-SH-X    3    0.75          0.0             3.         JCC,7,(1986),230
-371	X -C*-CB-X    4    6.70        180.0             2.         intrpol.bsd.onC6H6aa
-372	X -C*-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
-373	X -C*-CW-X    4   26.10        180.0             2.         intrpol.bsd.on C6H6
-374	X -CA-CN-X    4   14.50        180.0             2.         reinterpolated 93'
-375	X -CB-CN-X    4   12.00        180.0             2.         reinterpolated 93'
-376	X -CC-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
-377	X -CC-CV-X    4   20.60        180.0             2.         intrpol.bsd.on C6H6
-378	X -CC-CW-X    4   21.50        180.0             2.         intrpol.bsd.on C6H6
-379	X -CC-NA-X    4    5.60        180.0             2.         JCC,7,(1986),230
-380	X -CC-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
-381	X -CN-NA-X    4    6.10        180.0             2.         reinterpolated 93'
-382	X -CR-NA-X    4    9.30        180.0             2.         JCC,7,(1986),230
-383	X -CR-NB-X    2   10.00        180.0             2.         JCC,7,(1986),230
-384	X -CV-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
-385	X -CW-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
-386	CT-CT-OS-CT   1    0.383         0.0            -3.
-387	CT-CT-OS-CT   1    0.1         180.0             2.
-388	C -N -CT-C    1    0.20        180.0             2.
-389	N -CT-C -N    1    0.40        180.0            -4.
-390	N -CT-C -N    1    1.35        180.0            -2.
-391	N -CT-C -N    1    0.75        180.0             1.
-392	CT-CT-N -C    1    0.50        180.0            -4.
-393	CT-CT-N -C    1    0.15        180.0            -3.
-394	CT-CT-N -C    1    0.53          0.0             1.
-395	CT-CT-C -N    1    0.100         0.0            -4.
-396	CT-CT-C -N    1    0.07          0.0             2.
-397	H -N -C -O    1    2.50        180.0            -2.         JCC,7,(1986),230
-398	H -N -C -O    1    2.00          0.0             1.         J.C.cistrans-NMA DE
-399	CT-S -S -CT   1    3.50          0.0            -2.         JCC,7,(1986),230
-400	CT-S -S -CT   1    0.60          0.0             3.         JCC,7,(1986),230
-401	OS-CT-CT-OS   1    0.144         0.0            -3.         JCC,7,(1986),230
-402	OS-CT-CT-OS   1    1.00          0.0             2.         pucker anal (93')
-403	OS-CT-CT-OH   1    0.144         0.0            -3.         JCC,7,(1986),230
-404	OS-CT-CT-OH   1    1.00          0.0             2.         pucker anal (93')
-405	OH-CT-CT-OH   1    0.144         0.0            -3.         JCC,7,(1986),230
-406	OH-CT-CT-OH   1    1.00          0.0             2.         check glicolWC? puc
-407	OH-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
-408	OH-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
-409	OS-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
-410	OS-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
-411	OS-CT-N*-CK   1    0.50        180.0            -2.         sugar frag calc (PC)
-412	OS-CT-N*-CK   1    2.50          0.0             1.         sugar frag calc (PC)
-413	OS-CT-N*-CM   1    0.50        180.0            -2.         sugar frag calc (PC)
-414	OS-CT-N*-CM   1    2.50          0.0             1.         sugar frag calc (PC)
-415	
-416	X -X -C -O          10.5         180.          2.           JCC,7,(1986),230
-417	X -O2-C -O2         10.5         180.          2.           JCC,7,(1986),230
-418	X -X -N -H          1.0          180.          2.           JCC,7,(1986),230
-419	X -X -N2-H          1.0          180.          2.           JCC,7,(1986),230
-420	X -X -NA-H          1.0          180.          2.           JCC,7,(1986),230
-421	X -N2-CA-N2         10.5         180.          2.           JCC,7,(1986),230
-422	X -CT-N -CT         1.0          180.          2.           JCC,7,(1986),230
-423	X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes
-424	X -X -CW-H4         1.1          180.          2.
-425	X -X -CR-H5         1.1          180.          2.
-426	X -X -CV-H4         1.1          180.          2.
-427	X -X -CQ-H5         1.1          180.          2.
-428	X -X -CK-H5         1.1          180.          2.
-429	X -X -CM-H4         1.1          180.          2.
-430	X -X -CM-HA         1.1          180.          2.
-431	X -X -CA-H4         1.1          180.          2.           bsd.on C6H6 nmodes
-432	X -X -CA-H5         1.1          180.          2.           bsd.on C6H6 nmodes
-433	CK-CB-N*-CT         1.0          180.          2.
-434	CM-C -N*-CT         1.0          180.          2.           dac guess, 9/94
-435	CM-C -CM-CT         1.1          180.          2.
-436	CT-O -C -OH         10.5         180.          2.
-437	NA-CV-CC-CT         1.1          180.          2.
-438	NB-CW-CC-CT         1.1          180.          2.
-439	NA-CW-CC-CT         1.1          180.          2.
-440	CW-CB-C*-CT         1.1          180.          2.
-441	CA-CA-CA-CT         1.1          180.          2.
-442	C -CM-CM-CT         1.1          180.          2.           dac guess, 9/94
-443	NC-CM-CA-N2         1.1          180.          2.           dac guess, 9/94
-444	CB-NC-CA-N2         1.1          180.          2.           dac, 10/94
-445	NA-NC-CA-N2         1.1          180.          2.           dac, 10/94
-446	CA-CA-C -OH         1.1          180.          2.
-447	
-448	  HW  OW  0000.     0000.                                4.  flag for fast water
-449	
-450	N   NA  N2  N*  NC  NB  N3  NP  NO
-451	C   C*  CA  CB  CC  CN  CM  CK  CQ  CW  CV  CR  CA  CX  CY  CD
-452	
-453	MOD4      RE
-454	  H           0.6000  0.0157            !Ferguson base pair geom.
-455	  HO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657
-456	  HS          0.6000  0.0157             W. Cornell CH3SH --> CH3OH FEP
-457	  HC          1.4870  0.0157             OPLS
-458	  H1          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
-459	  H2          1.2870  0.0157             Veenstra et al JCC,8,(1992),963
-460	  H3          1.1870  0.0157             Veenstra et al JCC,8,(1992),963
-461	  HP          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
-462	  HA          1.4590  0.0150             Spellmeyer
-463	  H4          1.4090  0.0150             Spellmeyer, one electrowithdr. neighbor
-464	  H5          1.3590  0.0150             Spellmeyer, two electrowithdr. neighbor
-465	  HW          0.0000  0.0000             TIP3P water model
-466	  O           1.6612  0.2100             OPLS
-467	  O2          1.6612  0.2100             OPLS
-468	  OW          1.7683  0.1520             TIP3P water model
-469	  OH          1.7210  0.2104             OPLS
-470	  OS          1.6837  0.1700             OPLS ether
-471	  CT          1.9080  0.1094             Spellmeyer
-472	  CA          1.9080  0.0860             Spellmeyer
-473	  CM          1.9080  0.0860             Spellmeyer
-474	  C           1.9080  0.0860             OPLS
-475	  N           1.8240  0.1700             OPLS
-476	  S           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
-477	  SH          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
-478	  P           2.1000  0.2000             JCC,7,(1986),230;
-479	  IM          2.47    0.1                Cl- Smith & Dang, JCP 1994,100:5,3757
-480	  Li          1.1370  0.0183             Li+ Aqvist JPC 1990,94,8021. (adapted)
-481	  IP          1.8680  0.00277            Na+ Aqvist JPC 1990,94,8021. (adapted)
-482	  K           2.6580  0.000328           K+  Aqvist JPC 1990,94,8021. (adapted)
-483	  Rb          2.9560  0.00017            Rb+ Aqvist JPC 1990,94,8021. (adapted)
-484	  Cs          3.3950  0.0000806          Cs+ Aqvist JPC 1990,94,8021. (adapted)
-485	  I           2.35    0.40               JCC,7,(1986),230; 
-486	  F           1.75    0.061              Gough et al. JCC 13,(1992),963.
-487	  IB          5.0     0.1                solvated ion for vacuum approximation
-488	 
-489	END
-490	END

File src/main/resources/cml/forcefield/amber/parm94.xml

-<list
-  id='parm94' 
-  output="VERBOSE"
-  convention='conventions:compchem'
-  xmlns:conventions="http://www.xml-cml.org/convention/"  
-  
-  xmlns:ff="http://www.xml-cml.org/dictionary/forcefield/"
-  xmlns:amber="http://www.xml-cml.org/dictionary/forcefield/amber"
-  xmlns:x="http://www.xml-cml.org/dictionary/cmlx/"
-  xmlns:h="http://www.w3.org/1999/xhtml"
-  
-  xmlns:m='http://www.w3.org/1998/Math/MathML'
-  xmlns="http://www.xml-cml.org/schema"
-  xmlns:xi="http://www.w3.org/2001/XInclude"
->
-    <scalar dictRef='ff:title'>PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs</scalar>
-
-    <list title="atoms" dictRef='ff:atoms'>
-        <list id='at2'>
-            <atomType dictRef='amber:parm94Type'>BR</atomType>
-            <scalar dictRef='ff:atmass'>79.90</scalar>
-            <scalar dictRef='ff:desc'>bromine</scalar>
-        </list>
-        <list id='at3'>
-            <atomType dictRef='amber:parm94Type'>C</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C carbonyl group</scalar>
-        </list>
-        <list id='at4'>
-            <atomType dictRef='amber:parm94Type'>CA</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C pure aromatic (benzene)</scalar>
-        </list>
-        <list id='at5'>
-            <atomType dictRef='amber:parm94Type'>CB</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 aromatic C, 5&amp;6 membered ring junction</scalar>
-        </list>
-        <list id='at6'>
-            <atomType dictRef='amber:parm94Type'>CC</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 aromatic C, 5 memb. ring HIS</scalar>
-        </list>
-        <list id='at7'>
-            <atomType dictRef='amber:parm94Type'>CK</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C 5 memb.ring in purines</scalar>
-        </list>
-        <list id='at8'>
-            <atomType dictRef='amber:parm94Type'>CM</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C pyrimidines in pos. 5 &amp; 6</scalar>
-        </list>
-        <list id='at9'>
-            <atomType dictRef='amber:parm94Type'>CN</atomType>
-            <scalar dictRef='ff:atmass'>12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C aromatic 5&amp;6 memb.ring junct.(TRP)</scalar>
-        </list>
-        <list id='at10'>
-            <atomType dictRef='amber:parm94Type'>CQ</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 C in 5 mem.ring of purines between 2 N</scalar>
-        </list>
-        <list id='at11'>
-            <atomType dictRef='amber:parm94Type'>CR</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 arom as CQ but in HIS</scalar>
-        </list>
-        <list id='at12'>
-            <atomType dictRef='amber:parm94Type'>CT</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp3 aliphatic C</scalar>
-        </list>
-        <list id='at13'>
-            <atomType dictRef='amber:parm94Type'>CV</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)</scalar>
-        </list>
-        <list id='at14'>
-            <atomType dictRef='amber:parm94Type'>CW</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)</scalar>
-        </list>
-        <list id='at15'>
-            <atomType dictRef='amber:parm94Type'>C*</atomType>
-            <scalar dictRef='ff:atmass'> 12.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 arom. 5 memb.ring w/1 subst. (TRP)</scalar>
-        </list>
-        <list id='at16'>
-            <atomType dictRef='amber:parm94Type'>C0</atomType>
-            <scalar dictRef='ff:atmass'> 40.08</scalar>
-            <scalar dictRef='ff:desc'>calcium</scalar>
-        </list>
-        <list id='at17'>
-            <atomType dictRef='amber:parm94Type'>F</atomType>
-            <scalar dictRef='ff:atmass'> 19.00</scalar>
-            <scalar dictRef='ff:desc'>fluorine</scalar>
-        </list>
-        <list id='at18'>
-            <atomType dictRef='amber:parm94Type'>H</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H bonded to nitrogen atoms</scalar>
-        </list>
-        <list id='at19'>
-            <atomType dictRef='amber:parm94Type'>HC</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H aliph. bond. to C without electrwd.group</scalar>
-        </list>
-        <list id='at20'>
-            <atomType dictRef='amber:parm94Type'>H1</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H aliph. bond. to C with 1 electrwd. group</scalar>
-        </list>
-        <list id='at21'>
-            <atomType dictRef='amber:parm94Type'>H2</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H aliph. bond. to C with 2 electrwd.groups</scalar>
-        </list>
-        <list id='at22'>
-            <atomType dictRef='amber:parm94Type'>H3</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H aliph. bond. to C with 3 eletrwd.groups</scalar>
-        </list>
-        <list id='at23'>
-            <atomType dictRef='amber:parm94Type'>HA</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H arom. bond. to C without elctrwd. groups</scalar>
-        </list>
-        <list id='at24'>
-            <atomType dictRef='amber:parm94Type'>H4</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H arom. bond. to C with 1 electrwd. group</scalar>
-        </list>
-        <list id='at25'>
-            <atomType dictRef='amber:parm94Type'>H5</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H arom. bond. to C with 2 electrwd. groups</scalar>
-        </list>
-        <list id='at26'>
-            <atomType dictRef='amber:parm94Type'>HO</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>hydroxyl group</scalar>
-        </list>
-        <list id='at27'>
-            <atomType dictRef='amber:parm94Type'>HS</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>hydrogen bonded to sulphur</scalar>
-        </list>
-        <list id='at28'>
-            <atomType dictRef='amber:parm94Type'>HW</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H in TIP3P water</scalar>
-        </list>
-        <list id='at29'>
-            <atomType dictRef='amber:parm94Type'>HP</atomType>
-            <scalar dictRef='ff:atmass'> 1.008</scalar>
-            <scalar dictRef='ff:desc'>H bonded to C next to positively charged gr</scalar>
-        </list>
-        <list id='at30'>
-            <atomType dictRef='amber:parm94Type'>I</atomType>
-            <scalar dictRef='ff:atmass'> 126.9</scalar>
-            <scalar dictRef='ff:desc'>iodine</scalar>
-        </list>
-        <list id='at31'>
-            <atomType dictRef='amber:parm94Type'>IM</atomType>
-            <scalar dictRef='ff:atmass'> 35.45</scalar>
-            <scalar dictRef='ff:desc'>assumed to be Cl-</scalar>
-        </list>
-        <list id='at32'>
-            <atomType dictRef='amber:parm94Type'>IP</atomType>
-            <scalar dictRef='ff:atmass'> 22.99</scalar>
-            <scalar dictRef='ff:desc'>assumed to be Na+</scalar>
-        </list>
-        <list id='at33'>
-            <atomType dictRef='amber:parm94Type'>IB</atomType>
-            <scalar dictRef='ff:atmass'> 131.0</scalar>
-            <scalar dictRef='ff:desc'>'big ion w/ waters' for vacuum (Na+, 6H2O)</scalar>
-        </list>
-        <list id='at34'>
-            <atomType dictRef='amber:parm94Type'>MG</atomType>
-            <scalar dictRef='ff:atmass'> 24.305</scalar>
-            <scalar dictRef='ff:desc'>magnesium</scalar>
-        </list>
-        <list id='at35'>
-            <atomType dictRef='amber:parm94Type'>N</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 nitrogen in amide groups</scalar>
-        </list>
-        <list id='at36'>
-            <atomType dictRef='amber:parm94Type'>NA</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 N in 5 memb.ring w/H atom (HIS)</scalar>
-        </list>
-        <list id='at37'>
-            <atomType dictRef='amber:parm94Type'>NB</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)</scalar>
-        </list>
-        <list id='at38'>
-            <atomType dictRef='amber:parm94Type'>NC</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 N in 6 memb.ring w/LP (ADE,GUA)</scalar>
-        </list>
-        <list id='at39'>
-            <atomType dictRef='amber:parm94Type'>N2</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 N in amino groups</scalar>
-        </list>
-        <list id='at40'>
-            <atomType dictRef='amber:parm94Type'>N3</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp3 N for charged amino groups (Lys, etc)</scalar>
-        </list>
-        <list id='at41'>
-            <atomType dictRef='amber:parm94Type'>N*</atomType>
-            <scalar dictRef='ff:atmass'> 14.01</scalar>
-            <scalar dictRef='ff:desc'>sp2 N</scalar>
-        </list>
-        <list id='at42'>
-            <atomType dictRef='amber:parm94Type'>O</atomType>
-            <scalar dictRef='ff:atmass'> 16.00</scalar>
-            <scalar dictRef='ff:desc'>carbonyl group oxygen</scalar>
-        </list>
-        <list id='at43'>
-            <atomType dictRef='amber:parm94Type'>OW</atomType>
-            <scalar dictRef='ff:atmass'> 16.00</scalar>
-            <scalar dictRef='ff:desc'>oxygen in TIP3P water</scalar>
-        </list>
-        <list id='at44'>
-            <atomType dictRef='amber:parm94Type'>OH</atomType>
-            <scalar dictRef='ff:atmass'> 16.00</scalar>
-            <scalar dictRef='ff:desc'>oxygen in hydroxyl group</scalar>
-        </list>
-        <list id='at45'>
-            <atomType dictRef='amber:parm94Type'>OS</atomType>
-            <scalar dictRef='ff:atmass'> 16.00</scalar>
-            <scalar dictRef='ff:desc'>ether and ester oxygen</scalar>
-        </list>
-        <list id='at46'>
-            <atomType dictRef='amber:parm94Type'>O2</atomType>
-            <scalar dictRef='ff:atmass'> 16.00</scalar>
-            <scalar dictRef='ff:desc'>carboxyl and phosphate group oxygen</scalar>
-        </list>
-        <list id='at47'>
-            <atomType dictRef='amber:parm94Type'>P</atomType>
-            <scalar dictRef='ff:atmass'> 30.97</scalar>
-            <scalar dictRef='ff:desc'>phosphate</scalar>
-        </list>
-        <list id='at48'>
-            <atomType dictRef='amber:parm94Type'>S</atomType>
-            <scalar dictRef='ff:atmass'> 32.06</scalar>
-            <scalar dictRef='ff:desc'>sulphur in disulfide linkage</scalar>
-        </list>
-        <list id='at49'>
-            <atomType dictRef='amber:parm94Type'>SH</atomType>
-            <scalar dictRef='ff:atmass'> 32.06</scalar>
-            <scalar dictRef='ff:desc'>sulphur in cystine</scalar>
-        </list>
-        <list id='at50'>
-            <atomType dictRef='amber:parm94Type'>CU</atomType>
-            <scalar dictRef='ff:atmass'> 63.55</scalar>
-            <scalar dictRef='ff:desc'>copper</scalar>
-        </list>
-        <list id='at51'>
-            <atomType dictRef='amber:parm94Type'>FE</atomType>
-            <scalar dictRef='ff:atmass'> 55.00</scalar>
-            <scalar dictRef='ff:desc'>iron</scalar>
-        </list>
-        <list id='at52'>
-            <atomType dictRef='amber:parm94Type'>Li</atomType>
-            <scalar dictRef='ff:atmass'> 6.94</scalar>
-            <scalar dictRef='ff:desc'>lithium</scalar>
-        </list>
-        <list id='at53'>
-            <atomType dictRef='amber:parm94Type'>K</atomType>
-            <scalar dictRef='ff:atmass'> 39.10</scalar>
-            <scalar dictRef='ff:desc'>potassium</scalar>
-        </list>
-        <list id='at54'>
-            <atomType dictRef='amber:parm94Type'>Rb</atomType>
-            <scalar dictRef='ff:atmass'> 85.47</scalar>
-            <scalar dictRef='ff:desc'>rubidium</scalar>
-        </list>
-        <list id='at55'>
-            <atomType dictRef='amber:parm94Type'>Cs</atomType>
-            <scalar dictRef='ff:atmass'> 132.91</scalar>
-            <scalar dictRef='ff:desc'>cesium</scalar>
-        </list>
-    </list>
-
-    <list title="bonds" dictRef='ff:bonds'>