# Put 1GID.shifted.pdb in last.1.pdb
firstStage 2    
lastStage 2   
reportingInterval .5    
numReportingIntervals  60  

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

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


mobilizer Rigid       Q 220 253        
contact AllHeavyAtomSterics        C 146 164          

#Threading forces
threading C 146 150 Q 222 226 300
threading C 160 164 Q 247 251 300

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