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 decoys/T0240.try1-opt2.pdb
NameTarget T0240

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time


ReadFragmentAlignment NOFILTER 1ihrA/1ihrA-T0240.2mer-a2m
PrintMultimerPDB 2 dimer-1ihrA-try1.pdb
Time