verbose 0
twoTransformForceMultiplier 100
loadTinkerParameterFile 0
sequence A          AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA                
sequence B          UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU                
sequence C      A                
sequence D      U                
sequence E      A                
sequence F      U                
-PRIOR 0
#-SQ B     AAAAAAAAACCCCUUUUUUUUU   
addNASTForces 0
periodicallyUpdateParameters 0
backboneOxygenGlobalCoulombScaleFactor 0  
backboneOxygenGlobalVdwScaleFactor 0  
#addBackboneOxygenForces 0
numMagnesiumIons  0
#addBackboneOxygenForces 0
maxReportingIntervals  100
reportingInterval  .2
scrubberPeriod  4 
prioritize 0
setForceScrubber 0
firstStage 1 
lastStage 1 
# torsion = 2 rigid =3

leontisWesthofInFileName /Users/Sam/svn/RNAToolbox/include/resources/parameters.csv  

addHuntCrossleySpheres 0
piecewiseRigidify 0
loopBondMobility 1
helixBondMobility 3 
overallBondMobility 1
setOverallBondMobility 0
setLoopBondMobility 0
setForceAndStericScrubber 0
rigidifyFormedHelices 0
rigidifyTermini 0
weldToGround 0


-FRN A 7 
-FRN B 7 
-FRN C 7 
-FRN D 7 
-FRN E 7 
-FRN F 7 


#-FRN B 1 
cutoffRadius .1 
readPreviousFrameFile 1
readInQVector 0
# -FS 1 
-T 1000 1
-T  500 2
-T  250 3
-T  100 4
-T   50 5
-T   10 6
-T   10 7
-DC .5 20
-DC 1. 1
-DC 1. 5

#twoTransformForce A 7 HelicalStackingA3 A 8 HelicalStackingA5 Cis 1
#twoTransformForce B 7 HelicalStackingA3  B 8 HelicalStackingA5 Cis 1
# twoTransformForce A 8 WatsonCrick A 15 WatsonCrick Cis 1
# twoTransformForce A 9 WatsonCrick A 14 WatsonCrick Cis 1

# twoTransformForce B 7 WatsonCrick B 16 WatsonCrick Cis 1
# twoTransformForce B 8 WatsonCrick B 15 WatsonCrick Cis 1
# twoTransformForce B 9 WatsonCrick B 14 WatsonCrick Cis 1

# twoTransformForce A 10 Custom  B 10 Custom Cis 1
#twoTransformForce A 7 WatsonCrick B 8 WatsonCrick Cis 1
#twoTransformForce A 8 WatsonCrick B 7 WatsonCrick Cis 1

#aromatic          A 7 Stacking3 B 7 Stacking5 Rotatable 1
#aromatic          C 7 Stacking3 D 7 Stacking3 Rotatable 1
#aromatic          E 7 Stacking5	F 7 Stacking5 Rotatable 1

baseInteraction   A 7 WatsonCrick B 7 WatsonCrick Cis     1
baseInteraction   C 7 WatsonCrick D 7 WatsonCrick Cis     1
baseInteraction   E 7 WatsonCrick F 7 WatsonCrick Cis     1

globalCoulombScaleFactor 0.0 1 
globalVdwScaleFactor 0.0 1