protein A 1 DIELTQSPATLSVTPGDSVSLSCRASQSISNGLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
protein B 1 QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC
protein E 1         KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
removeRigidBodyMomentum FALSE
mobilizer Rigid A 1 29
mobilizer Rigid A 35 214
mobilizer Rigid B 1 218

constrainToGround A 1
constrainToGround A 214
constrainToGround B 1

#MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME 
firstStage 2 

lastStage 2
smallGroupInertiaMultiplier 11  
reportingInterval .1
numReportingIntervals 150 
#useOpenMMAcceleration true

readAtStage 2

globalBondTorsionScaleFactor 1
globalBondBendScaleFactor 1
globalCoulombScaleFactor 1
globalVdwScaleFactor 1
globalAmberImproperTorsionScaleFactor 1
readBlockEnd

readAtStage 3
globalBondTorsionScaleFactor 0
globalBondStretchScaleFactor 0
globalBondBendScaleFactor 0
globalCoulombScaleFactor 1
globalVdwScaleFactor 0
globalAmberImproperTorsionScaleFactor 0

numReportingIntervals 1   
readBlockEnd



#light chain:
#protein A 1        DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSASWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

#heavy chain:
#protein B 1        QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

#protein E 1         KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
randomizeInitialVelocities false
#removeRigidBodyMomentum FALSE

physicsWhereYouWantIt true

#residues within 3 Angstroms of chain A resid 92:  32A, 47E, 49E, 90A
# residues within 5 Ångströms of chain A resid 92: 29-30A , 32A, 46-50E, 90-93A, 94A, 96A
# residues within 7 Ångströms of chain A resid 92:  27-28A 31A , 2A, 89A, 48E, 

readFromStage 1    
#within 7 of any potential mutation
includeAllNonBondAtomsInResidues A 2  2
includeAllNonBondAtomsInResidues A 27 34 
includeAllNonBondAtomsInResidues A 49 51
includeAllNonBondAtomsInResidues A 71 71
includeAllNonBondAtomsInResidues A 89 96

includeAllNonBondAtomsInResidues B 101 101
includeAllNonBondAtomsInResidues B 25  33 
includeAllNonBondAtomsInResidues B 48  71 
includeAllNonBondAtomsInResidues B 77 77
includeAllNonBondAtomsInResidues B 98 99

includeAllNonBondAtomsInResidues E 41  43
includeAllNonBondAtomsInResidues E 45   50 
includeAllNonBondAtomsInResidues E 53 53
includeAllNonBondAtomsInResidues E 65  70 
includeAllNonBondAtomsInResidues E 79  81
includeAllNonBondAtomsInResidues E 84 84


readBlockEnd


mobilizer Rigid E 1  129
constrainToGround E 1  

#within 7 of ((chain A and (resid 92 or resid 32)) )
#mobilizer Rigid A 1 214
#constrainToGround A 1

#within 7 of  (chain B and (resid 28 or resid 31 or resid 57 or resid  58 or resid 65 or resid 31))
#mobilizer Rigid B 1  28 
#mobilizer Rigid B 34 218
#constrainToGround B 1
#constrainToGround B 34


#waterDroplet D  50.0 9.0 69.0 5