firstStage 2 
lastStage  3 

readAtStage 2
# Template, 1WDN       
loadSequencesFromPdb 1WDN.short.pdb
# Old way, one could specify the sequence explicitly:
#protein B 4  KLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPKQ

# Model, 1GGG
loadSequencesFromPdb 1GGG.short.pdb
# Old way, one could specify the sequence explicitly:
#protein A 5   LVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTE

readBlockEnd

readAtStage 3
loadSequencesFromPdb
readBlockEnd

alignmentForces noGap
alignmentForces  A 5 224 B 5 224
#threading A 5 224 B 5 224 

# you will want to reduce this if you remove the mobilizer .. Rigid commands.
removeRigidBodyMomentum false
temperature 1.0 

# make all chains (A and B) Rigid along their full lengths:
mobilizer Rigid 



# Rigid alignment stage
readAtStage 2
deactivatePhysics A
deactivatePhysics B
# This stage is short, will converge after 60 ps or so:    
reportingInterval 10.0
numReportingIntervals 6
# Do nothing.  All chains will be left fully rigid.
#mobilizer Rigid A 5 224
readBlockEnd

readAtStage 3

reportingInterval 1.0
numReportingIntervals 25
# Flexibilize just the hinges on your model:
mobilizer Default A 87+1 90-1
mobilizer Default A 180+1 184-1
# The N- and C-termini are in the same, discontinuous domain. Constrain them to each other, otherwise the domain would fall apart:
constraint A FirstResidue Weld A LastResidue


setDefaultMDParameters
physicsRadius .7
# Turn off physics for the template chain:
deactivatePhysics B


#mobilizer Rigid A 5 87
#mobilizer Rigid A 90 180
#mobilizer Rigid A 184 224
#constrainToGround A 5
#constrainToGround A 195

readBlockEnd