setTemperature 1
#loopBondMobility 1
sequence A          AAAAAAAAAA
#sequence B          UUUUUUUUUU
twoTransformForceMultiplier 100
@myFirstRes 1.
firstResidueNumber A @myFirstRes
#firstResidueNumber B 101
#temperature 300 2
#temperature 100 3
#temperature 10 4
#dutyCycle .5 3
#dutyCycle 1 5
excludedVolumeStiffness  10000  # was 	1e+07
excludedVolumeRadius           .12500  # was 	.125  
#kbBackboneTorsionGlobalScaleFactor 1
temperature  1.   1
temperature  1 2 #350.0 2
temperature  125.0 3
temperature   60.0 4
temperature  30.00 5
temperature  10. 6
dutyCycle .5 2
dutyCycle 1. 6
dutyCycle 1. 1
#addAllHeavyAtomSterics TRUE


firstStage 1          
lastStage 1           
globalCoulombScaleFactor 0.0 
globalVdwScaleFactor 0.0 
leontisWesthofInFileName /Users/Sam/svn/RNAToolbox/include/resources/parameters.csv
maxReportingIntervals 100
reportingInterval  4 
#constrainToGround A 1
#contact A 1 AllHeavyAtomSterics A 10 AllHeavyAtomSterics Cis 1
#contact B 1 AllHeavyAtomSterics B 10 AllHeavyAtomSterics Cis 1

#springToGround A 1  C1* 0.0 0.0 28.0
#springToGround A 10 C1* 0.0 0.0 0.0 
#baseInteraction A 1 WatsonCrick A 10 WatsonCrick Cis 1
#baseInteraction A 2 WatsonCrick A   9 WatsonCrick Cis 1
#baseInteraction A 3 WatsonCrick A   8 WatsonCrick Cis 1

readFromStage 100 

baseInteraction A 1 HelicalStackingA3 A 2  HelicalStackingA5 Cis 1
baseInteraction A 2 HelicalStackingA3 A 3 HelicalStackingA5 Cis 1
baseInteraction A 3 HelicalStackingA3 A 4 HelicalStackingA5 Cis 1
baseInteraction A 4 HelicalStackingA3 A 5 HelicalStackingA5 Cis 1
baseInteraction A 5 HelicalStackingA3 A 6 HelicalStackingA5 Cis 1
baseInteraction A 6 HelicalStackingA3 A 7 HelicalStackingA5 Cis 1
baseInteraction A 7 HelicalStackingA3 A 8 HelicalStackingA5 Cis 1
baseInteraction A 8 HelicalStackingA3 A 9 HelicalStackingA5 Cis 1
baseInteraction A 9 HelicalStackingA3 A 10 HelicalStackingA5 Cis 1

baseInteraction B 1 HelicalStackingA3 B 2  HelicalStackingA5 Cis 1
baseInteraction B 2 HelicalStackingA3 B 3 HelicalStackingA5 Cis 1
baseInteraction B 3 HelicalStackingA3 B 4 HelicalStackingA5 Cis 1
baseInteraction B 4 HelicalStackingA3 B 5 HelicalStackingA5 Cis 1
baseInteraction B 5 HelicalStackingA3 B 6 HelicalStackingA5 Cis 1
baseInteraction B 6 HelicalStackingA3 B 7 HelicalStackingA5 Cis 1
baseInteraction B 7 HelicalStackingA3 B 8 HelicalStackingA5 Cis 1
baseInteraction B 8 HelicalStackingA3 B 9 HelicalStackingA5 Cis 1
baseInteraction B 9 HelicalStackingA3 B 10 HelicalStackingA5 Cis 1

readBlockEnd

readFromStage 100 
baseInteraction A 1 HelicalStackingA3 A 2  HelicalStackingA5 Cis 1
baseInteraction B 9 HelicalStackingA3 B 10 HelicalStackingA5 Cis 1
readBlockEnd
readFromStage 100 
baseInteraction A 1 WatsonCrick B 110 WatsonCrick Cis 1
baseInteraction A 2 WatsonCrick B 109 WatsonCrick Cis 1
baseInteraction A 3 WatsonCrick B 108 WatsonCrick Cis 1
baseInteraction A 4 WatsonCrick B 107 WatsonCrick Cis 1
baseInteraction A 5 WatsonCrick B 106 WatsonCrick Cis 1
baseInteraction A 6 WatsonCrick B 105 WatsonCrick Cis 1
baseInteraction A 7 WatsonCrick B 104 WatsonCrick Cis 1
baseInteraction A 8 WatsonCrick B 103 WatsonCrick Cis 1
baseInteraction A 9 WatsonCrick B 102 WatsonCrick Cis 1
baseInteraction A 10 WatsonCrick B 101 WatsonCrick Cis 1

readBlockEnd