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loadSequencesFromPdb 1ARJ.short.pdb
#RNA N 17 GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
removeRigidBodyMomentum False
constrainToGround N 17
mobilizer Rigid N 17 21
mobilizer Rigid N 27 38
mobilizer Rigid N 41 45
constraint N 17 Weld N 45
constraintTolerance .001
contact SelectedAtoms N FirstResidue LastResidue
numReportingIntervals 5
reportingInterval 2.0
firstStage 1
lastStage 1
temperature 30.0
baseInteraction N 26 WatsonCrick N 39 WatsonCrick Cis
baseInteraction N 22 WatsonCrick N 40 WatsonCrick Cis
baseInteraction N 27 WatsonCrick N 38 WatsonCrick Cis
baseInteraction N 28 WatsonCrick N 37 WatsonCrick Cis
baseInteraction N 29 WatsonCrick N 36 WatsonCrick Cis
baseInteraction N 17 WatsonCrick N 45 WatsonCrick Cis
baseInteraction N 18 WatsonCrick N 44 WatsonCrick Cis
baseInteraction N 19 WatsonCrick N 43 WatsonCrick Cis
baseInteraction N 20 WatsonCrick N 42 WatsonCrick Cis
baseInteraction N 21 WatsonCrick N 41 WatsonCrick Cis
globalCoulombScaleFactor 1
globalVdwScaleFactor 1
smallGroupInertiaMultiplier 11
setInitialVelocities TRUE
#includeAllResiduesWithin 1.0 N 33
includeAllNonBondAtomsInResidues N 27 30
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