firstStage 2    
lastStage 2   
reportingInterval 2.    
maxReportingIntervals  60  

# TETRAHYMENA P6ab -- "target" fragment  
RNA Q 220 GUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAU

# AZOARCUS -- "threaded" fragment   
RNA      C 146 CCUAAGGCAAACGCUAUGG                                              


mobilizer       Q 220 Rigid Q 253        
contact         C 146 SelectedAtoms C 164          

#Threading forces
baseInteractionForceMultiplier 10

baseInteraction C 146 Superimpose Q 222 Superimpose Cis 2  
baseInteraction C 147 Superimpose Q 223 Superimpose Cis 2  
baseInteraction C 148 Superimpose Q 224 Superimpose Cis 2  
baseInteraction C 149 Superimpose Q 225 Superimpose Cis 2  
baseInteraction C 150 Superimpose Q 226 Superimpose Cis 2  
baseInteraction C 160 Superimpose Q 247 Superimpose Cis 2   
baseInteraction C 161 Superimpose Q 248 Superimpose Cis 2  
baseInteraction C 162 Superimpose Q 249 Superimpose Cis 2  
baseInteraction C 163 Superimpose Q 250 Superimpose Cis 2  
baseInteraction C 164 Superimpose Q 251 Superimpose Cis 2