SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-1332.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

# ReadTargetPDB T0240-1ihrA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5.pdb
# ReadTargetPDB T0240-1ihrA-crude-monomer.pdb 
ReadTargetPDB ../decoys/monomer-from-dimer-chimera-9.pdb 
NameTarget T0240

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time

AddId 1ihrA 
AddId 1ihrB
ReadTemplatePDBIds 

InFilePrefix ../1ihrA/
ReadFragmentAlignment NOFILTER 1ihrA-dimer.a2m
InFilePrefix
PrintMultimerPDB 2 dimer-try9.pdb
Time