# Model, 1GGG
protein A 5   LVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTE
# Target, 1WDN       
protein B 4  KLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPKQ
#calcEnergy false
proteinThreading 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 B 4   Rigid B 227

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

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

temperature 1.0 1