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/T0223.try4-opt2.pdb
NameTarget T0223

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time

# If multimer is not already in pdb, but needs crystal symmetries to generate,
# then fetch the "biological unit" from pdb and use the following commands:
// ReadTemplatePDB 1bkj.pdb1 model 1 name 1bkjA
// ReadTemplatePDB 1bkj.pdb1 model 2 name 1bkjB

InFilePrefix 1bkjA/
ReadFragmentAlignment NOFILTER T0223-1bkjA.2mer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-1bkjA-try4.pdb
Time