File: commands.singlebasepair.dat

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calcEnergy true
RNA A 1 AGGGGU
firstStage 1
lastStage 1
baseInteractionScaleFactor     100
temperature 30.0 
contact AllHeavyAtomSterics A FirstResidue LastResidue
#addSelectedAtoms true
baseInteraction A 1 WatsonCrick A 6 WatsonCrick Cis  

reportingInterval 1.0