#loadSequencesFromPdb
removeRigidBodyMomentum false


RNA M 1 CCUAUCAAUGAUAGA
RNA N 1 UCUAUCAUUGAUAGG
RNA m 1 CCUAUCAAUGAUAGA
RNA n 1 UCUAUCAUUGAUAGG
protein A 4 LNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ
protein a 4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHKDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAILAVIHFTLGAVLEQQEHTAALTDRPAAPDTDAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ

numReportingIntervals 140
firstStage 2 
lastStage 2
mobilizer Rigid
constrainToGround M FirstResidue
constrainToGround N FirstResidue
constraint A FirstResidue Weld a FirstResidue
constraint A FirstResidue Weld m FirstResidue
constraint A FirstResidue Weld n FirstResidue

threading m FirstResidue LastResidue-1 M FirstResidue+1 LastResidue 300
threading n FirstResidue+1 LastResidue N FirstResidue LastResidue-1 300