SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-40pc-3157.rot

Time


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

InFilePrefix 

# ReadTargetPDB XXX0000.blank.pdb
ReadTargetSeq XXX0000.a2m START_COL
NameTarget XXX0000
PopConform

Time

InFilePrefix
include costfcn-init.under
include try1.costfcn
Time

// include all previously found decoys!
InFilePrefix decoys/
include read-pdb.under
Time

OutFilePrefix decoys/
ReportCost score-all.try1.rdb
CostConform
Time

PrintConformBreaks all.breaks
ClashConform all.clashes
Time

# print out the constraints, to verify that the requested ones were
# 	actually the ones desired.
# PrintConstraints

quit