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#MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME
#light chain (WT sequence):
protein A 1 DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
#heavy chain:
protein B 1 QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC
#antigen
protein E 1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
# Residue at chain A position 32 will be mutated from N to N. In other words, nothing will be done. But itäs good to change exactly one thing in WT vs mutant run.
substituteResidue A 32 N
removeRigidBodyMomentum FALSE
mobilizer Rigid
mobilizer Default A 32-2 32+2
setDefaultMDParameters
# Physics zone includes all residues within 1.2 nm of the flexibility zone:
physicsRadius 1.2
# smallGroupInertiaMultiplier scales the inertia tensor by a constant, so fast spinning of tiny chemical groups don't drive down the time step size.
smallGroupInertiaMultiplier 11
# take all rigid segments in all chains and constrain them to ground:
constrainChainRigidSegments
firstStage 2
lastStage 2
reportingInterval .1
numReportingIntervals 150
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