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-2191.rot

Time


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

InFilePrefix 

 ReadTargetSeq T0389.a2m 1
 NameTarget T0389
// Now have a random conformation---use PopConform if you don't want it.
 PopConform

Include costfcn-init.under
Include everything.costfcn
Time

OutfilePrefix decoys/

# put believed-to-be-best decoy first
InFilePrefix decoys/
ReadConformPDB	TR389.pdb
SaveConformAsReal

SetRealCost real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \
	real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \
	knot 10 clens 200  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0.2

include read-pdb+servers.under
Time




OutFilePrefix
ReportCost TR389-compare.rdb
CostConform


Time

quit