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# use provided TetR.pdb
firstStage 2
lastStage 2
reportingInterval 1.0
numReportingIntervals 50
temperature 1.0
removeRigidBodyMomentum false
# TetR class D, bound to DNA
protein A 4 LNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ
protein B 4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHKDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAILAVIHFTLGAVLEQQEHTAALTDRPAAPDTDAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ
# ^insertion---^
DNA M 1 CCTATCAATGATAGA
DNA N 1 TCTATCATTGATAGG
threading A 4 155 B 4 155 300.0
threading A 156 198 B 169 211 300.0
mobilizer Rigid A 4 198
#mobilizer Rigid B 4 203
mobilizer Rigid B 4 22
mobilizer Rigid B 30 34
mobilizer Rigid B 50 155
mobilizer Rigid B 169 211
mobilizer Rigid M 1 15
mobilizer Rigid N 1 15
constrainToGround A 4
constrainToGround M 1
constrainToGround N 1
#constraint B 22 Weld B 30
#constraint B 30 Weld B 50
#constraint B 155 Weld B 169
#contBct M 1 AllHeBvyAtomSterics M 15
#contact N 1 AllHeavyAtomSterics N 15
#contact a 25 AllHeavyAtomSterics B 27
#contact B 35 AllHeBvyAtomSterics B 40
# DNA-interacting:
#
# 35 - 40
# 23 - 29
# 42
# 46 - 49
# I'm simplifying a bit. See mobilizers above. Hence:
# 23 - 29
# 35 - 49
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