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pPSKnC9G_U332
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pPSKnC9G_U332
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##CHAINS
# Target, chain C of 3Q1R (tRNA)
#RNA C 1 GGCCAGGUAGCUCAGUUGGUAGAGCACUGGAUAUGGGCACCCCCUAAGUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCACCA
# Model, 1F27 (pseudoknot, chain W)
#Wild type
#RNA W 3 ACCGUCAGAGGACACGGUU
#G mutant
#RNA W 3 ACCGUCGGAGGACACGGUU
#C mutant
RNA W 3 ACCGUCCGAGGACACGGUU
#U mutant
#RNA W 3 ACCGUCUGAGGACACGGUU
#Other chains to be moved along
# Chain Z of 1F27 (pseudoknot) + 5 extra nucleotides added to 3' end (to match pseudoknot used in the lab)
RNA Z 22 AAAAAGUCCUCGCCA
# Chain B of 3Q1R (RNase p RNA)
RNA B 1 GGAGAGGAGCAGGCGGUCGCGGGGGCGCACACCUGCGCUUCCCGAGGAAAGUCCGGACUCUGGAGCGGGGUGCCGGGUAACGCCCGGGAGGGGUGACCCUCGGACAGGGCCAUAGAGAAGAAGACCGCCCGGGGGGAAACUUCCGGGCAAGGGUGGAACGGUGGGGUAAGAGCCCACCAGCGUCGGGGCAACCCGGCGGCUUGGCAACCCCCACCUGGAGCAAGGCCAAGCAGGGGGUUGGGUCGCUCCCCCUAUUCCCCCGGGUUGGCCGCUUGAGGUGUGCGGUAACGCACACCCCAGAUUGAUGACCGCCCACGACAGAAUCCGGCUUAUGCUCCUCUCCCGUG
#Chain A of 3Q1R (RNase P protein cofactor)
#protein A 6 TRRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG
#Chain D of 3Q1R (tRNA 5’ leader)
#RNA D -5 GGCGU
#Mg ions
monoAtoms E 34 20 Mg+2
#STAGES
firstStage 7
lastStage 8
mobilizer Rigid
readFromStage 7
#matchPurineN1AtomLocations FALSE
#substituteResidue W 9 U
#substituteResidue W 12 C
#substituteResidue Z 30 G
matchPurineN1AtomLocations FALSE
substituteResidue B 304 U
forceMultiplier 400
baseInteraction W 10 WatsonCrick Z 32 WatsonCrick Cis
baseInteraction W 11 WatsonCrick Z 31 WatsonCrick Cis
baseInteraction W 12 WatsonCrick Z 30 WatsonCrick Cis
#baseInteraction W 13 WatsonCrick Z 29 WatsonCrick Cis
#baseInteraction W 14 WatsonCrick Z 28 WatsonCrick Cis
#baseInteraction W 15 WatsonCrick Z 27 WatsonCrick Cis
#baseInteraction W 7 WatsonCrick W 16 WatsonCrick Cis
#baseInteraction W 6 HelicalStackingA3 W 7 HelicalStackingA5 Cis
#baseInteraction W 16 HelicalStackingA3 W 17 HelicalStackingA5 Cis
mobilizer Default W 8 12
#mobilizer Default W 11 16
mobilizer Default Z 30 32
mobilizer Default B 50 53
#mobilizer Default B 52 52
mobilizer Default B 220 222
mobilizer Default B 304 304
mobilizer Default B 321 324
#constrainToGround W 10
#constrainToGround Z 32
constrainChainRigidSegments W Ground
constrainChainRigidSegments Z Ground
constrainChainRigidSegments B Ground
#psiPhiMobility Rigid
setDefaultMDParameters
physicsRadius .6
#includeResiduesWithin 1.2 W 9
#reportingInterval .01
readBlockEnd
readAtStage 7
reportingInterval .01
numReportingIntervals 1
#waterDroplet H 5.82 -2.385 1.2769 1.6 30000
waterDroplet H 6.41 -2.55 0.80 2.5 30000
#waterDroplet J 5.82 -3.385 1.2769 1.6 30000
readBlockEnd
readAtStage 8
reportingInterval .2
numReportingIntervals 100
#waterDroplet H 5.82 -2.385 1.2769 1.4 30000
waterDroplet H 6.41 -2.55 0.80 2.3 30000
#waterDroplet J 5.82 -3.385 1.2769 1.4 30000
readBlockEnd
removeRigidBodyMomentum false
#keeping it all together: mobilize and constrain to ground all chains belonging to the holoenzyme (chains A, B, C, D)
#rootMobilizer A Weld
#rootMobilizer C Weld
#rootMobilizer D Weld
constrainToGround B 1
#physics off for chain A (protein) and chains C, D (tRNA)
#deactivatePhysics A
#deactivatePhysics C
#deactivatePhysics D
randomizeInitialVelocities TRUE