# Target, 1WDN       
protein B 4  KLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPKQ

# Model, 1GGG
protein A 5   LVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTE
#calcEnergy false
threading A 5 224 B 5 224 
firstStage 2 
lastStage 3 

# you will want to reduce this if you remove the mobilizer .. Rigid commands.
reportingInterval 10.0
numReportingIntervals 25
removeRigidBodyMomentum false

mobilizer Rigid B 4    227

# Rigid alignment stage
readAtStage 2
mobilizer Rigid A 5 224
readBlockEnd

readAtStage 3
mobilizer Rigid A 5 87
mobilizer Rigid A 90 180
mobilizer Rigid A 184 224
constrainToGround A 5
constrainToGround A 195
readBlockEnd

temperature 1.0