# Instructions:
# copy 1BA2.aligned.pdb to last.1.pdb
# make sure you have 2DRI.5res.xplor in the working directory.
# Go!

#1BA2.short.pdb 
protein A 1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTRSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ

firstStage 2
lastStage 2

numReportingIntervals 100
reportingInterval .1

# Synthetic density map from 2DRI, at 5Å :
densityFileName 2DRI.5res.xplor
fitToDensity A
densityForceConstant 10

# Rigidify 
mobilizer Rigid

# Refer to the Flores and Gerstein FlexOracle paper:
# HAG hinges: 103 104 235 236

# Flexibilize the HAG hinge:
mobilizer Default A 102 104
mobilizer Default A 235 237
mobilizer Default A 263 268          
constraint A 101 Weld A 238

mobilizer Default A 67 70
mobilizer Default A 132 135
constraint A 66 Weld A 71
constraint A 131 Weld A 136

# Turn on PARM99 force field:
setDefaultMDParameters
globalCoulombScaleFactor .1

##### main hinge
includeResiduesWithin 1.0 A 103
includeResiduesWithin 1.0 A 104
includeResiduesWithin 1.0 A 235
includeResiduesWithin 1.0 A 236

#####  flexible terminal
includeResiduesWithin 1.0 A 263
includeResiduesWithin 1.0 A 264
includeResiduesWithin 1.0 A 265 
includeResiduesWithin 1.0 A 266
includeResiduesWithin 1.0 A 267
includeResiduesWithin 1.0 A 268 
includeResiduesWithin 1.0 A 269
includeResiduesWithin 1.0 A 270
includeResiduesWithin 1.0 A 271

##### cleft contacts
includeResiduesWithin 1.0 A 67 
includeResiduesWithin 1.0 A 68 
includeResiduesWithin 1.0 A 69 
includeResiduesWithin 1.0 A 70 
includeResiduesWithin 1.0 A 132
includeResiduesWithin 1.0 A 133
includeResiduesWithin 1.0 A 134
includeResiduesWithin 1.0 A 135