# By Eloy Vallina Estrada, Stockholm University
# With a wee bit of help from Sam

# BEGIN
firstStage 2
lastStage  2

# STAGE 2 - semi-rigid alignment
readAtStage 2

# antibody
loadSequencesFromPdb 1mlb.AB.pdb
# lysozyme
loadSequencesFromPdb 1dpx.C.pdb
# bound structure
loadSequencesFromPdb 1mlc.DEF.pdb

# Let's move 1MLB -3nm in X. Just to make the initial workspace look less cluttered. 
initialDisplacement A -3  0 0 
initialDisplacement B -3  0 0 

readBlockEnd

readAtStage 3
# At any further stages, read in sequences from last.n-1.pdb :
loadSequencesFromPdb
readBlockEnd



reportingInterval 1.0
numReportingIntervals 35 

# set the strenght of alignment springs:
alignmentForces forceConstant 300
# Pull targets ABC onto template chain DEF:
alignmentForces A   D
alignmentForces B   E
alignmentForces C   F

# Turn on the Coulomb and VdW terms of the force field:
setDefaultMDParameters
# Include only a few residues in the interface, in the force field:
includeResiduesWithin .60 A 32
includeResiduesWithin .60 A 93
includeResiduesWithin .60 B 33
includeResiduesWithin .60 C 68

# Always turn off physics for the template! Otherwise we wil not be able to pull the target onto it:
deactivatePhysics D
deactivatePhysics E
deactivatePhysics F

# Fix the template to ground. This command makes it so there is only a Rigid mobilizer between ground and the root atoms of DEF:
rootMobilizer D Weld
rootMobilizer E Weld
rootMobilizer F Weld

# The rigid body momentum remover sets overall momenta to zero and moves the center of mass to the origin. So we need to turn that off:
removeRigidBodyMomentum false

#Now rigidify all chains:
mobilizer Rigid
# We don't want the heavy and light chains of the antibody to separate or change relative conformation:
constraint A FirstResidue Weld B FirstResidue
# Since A and B are both rigid, the above choice of residue number is arbitrary.

# Chain C residue 4 clashes with chain A resid 94:
mobilizer Default C 45-1 45+1
# constrain the two rigid fragments thus generated:
constraint C 45-2 Weld C 45+2

temperature 1.0