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# 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
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