# To run this example, first copy antibody-antigen.pdb to last.1.pdb.
# The point of this example is not to compute accurate DDG -- just to demonstrate the use of the mobilizeInterfaces and psiPhiMobility commands and the physicsRadius parameter.
#MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME 
#light chain:
protein A 1         DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
#heavy chain:
protein B 1 QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC
#antigen
protein E 1         KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
substituteResidue A 32 G
removeRigidBodyMomentum FALSE
mobilizer Rigid 
# This sets the backbone bonds to Rigid. It is applied later than the "mobilizer" and "mobilizeInterfaces" commands, so prevails in case of conflict with those.  End result: even if the side chains are flexible, the whole backbone will be rigid.
psiPhiMobility Rigid
# this ensures that five residues surrounding the mutation are made flexible (at least the side chains -- again the backbone will be rigidified).
mobilizer Default A 32-2 32+2
# Now set the bond mobility to Default for all residues at the interface of chains A and B, with all other chains (in this case, just chain E).
mobilizeInterfaces .6 Default A B 
setDefaultMDParameters
# All residues within 1.2 nm of a "flexible" atom will be included in the physics zone:
physicsRadius 1.2

# To keep small groups (e.g. methyls) from spinning out of control, increase their moment of inertia:
smallGroupInertiaMultiplier 11  
# All rigid segments (in this case, each chain is one rigid segment, at least the backbone) will be fixed to ground:
constrainChainRigidSegments


firstStage 2 

lastStage 2
reportingInterval .1
numReportingIntervals 150 
#useOpenMMAcceleration true

randomizeInitialVelocities false