// 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 monomeric-50pc.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist


CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log
CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist
CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist

CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist
CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist
CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist

CreateAlphaCost alpha monomeric-smoothed-alpha.hist
CreateAlphaCost alpha_prev  monomeric-smoothed-alpha-1.hist -1

Time


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

InFilePrefix 

ReadTargetPDB T0137.blank.pdb
NameTarget T0137
PopConform	// get rid of uneeded all-zero conformation

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0137.t2k.alpha.rdb 2 alpha alpha_prev


// try to close up the barrel, which gaped a bit in T0137.try2-opt.pdb
Constraint 485	590	2.0 2.7 3.2	// N E62  O V74
Constraint 492	585	2.0 2.7 3.2	// O E62  N V74
Constraint 500	574	2.0 2.7 3.2	// N S64  O K72
Constraint 504	567	2.0 2.7 3.2	// O S64  N K72
Constraint 517	554	2.0 2.7 3.2	// N K66  O K70
Constraint 524	547	2.0 2.7 3.2	// O K66  N K70



SetCost gen6.5 0.2 wet6.5 0.2 dry5 1 dry6.5 8 dry8 4 dry12 1 \
	phobic_fit 0.5 \
	sidechain 0.2 \
	clashes 1 sidechain_clashes -0.2 backbone_clashes 0.5 \
	break 15  \
	constraints 0.02 \
	pred_alpha2 1 \
	contact_order 1

//	known_ssbond 0.5
//	radius_norm 0 radius_fit 0.2 \
// 	alpha 1 alpha_prev 1 \