# 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