forceMultiplier 10
globalBondStretchScaleFactor .01
globalBondBendScaleFactor .01
coarseNucleicAcidSequence A AAAAAAAAAA
coarseNucleicAcidSequence B UUUUUUUUUU
firstResidueNumber A 1
firstResidueNumber B 1
firstStage 1          
lastStage 6
addHardSphereSmall TRUE           
globalCoulombScaleFactor 0.0 1
globalVdwScaleFactor 0.0 1
dutyCycle .5 1
dutyCycle 1 6 
temperature 10 1
temperature 60 3
temperature 30 4
temperature 10 5
leontisWesthofInFileName /Users/Sam/svn/RNAToolbox/include/resources/parameters.csv
loadTinkerParameterFile TRUE
tinkerParameterFileName      /Users/Sam/svn/RNAToolbox/include/resources/tinker_amber99_sam.prm
maxReportingIntervals 100 
reportingInterval  2
#contact A 1 HardSphere  A 10 HardSphere  Cis 1
baseInteraction A 1 WatsonCrick B 10 WatsonCrick Cis 1
baseInteraction A 2 WatsonCrick B 9 WatsonCrick Cis 1
baseInteraction A 3 WatsonCrick B 8 WatsonCrick Cis 1
baseInteraction A 4 WatsonCrick B 7 WatsonCrick Cis 1
baseInteraction A 5 WatsonCrick B 6 WatsonCrick Cis 1
baseInteraction A 6 WatsonCrick B 5 WatsonCrick Cis 1
baseInteraction A 7 WatsonCrick B 4 WatsonCrick Cis 1
baseInteraction A 8 WatsonCrick B 3 WatsonCrick Cis 1
baseInteraction A 9 WatsonCrick B 2 WatsonCrick Cis 1
baseInteraction A 10 WatsonCrick B 1 WatsonCrick Cis 1