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/T0270.try2-opt2.pdb
NameTarget T0270

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 1t0t.pdb1 model 1 name 1t0tA
// ReadTemplatePDB 1t0t.pdb1 model 2 name 1t0tB

InFilePrefix 1t0tV/
ReadFragmentAlignment NOFILTER T0270-1t0t.5mer-a2m
InFilePrefix
PrintMultimerPDB 5 5mer-1t0tV-try2.pdb
Time