// 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 T0169.blank.pdb
NameTarget T0169
PopConform	// get rid of uneeded all-zero conformation

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0169.t2k.alpha.rdb 2 alpha alpha_prev

// Include try2.constraints
// Include try3.constraints
// include try6.constraints
// include try8.constraints
// include try9.constraints
// include try10.constraints
// include try11.constraints
// include try12.constraints
// include try13.constraints
// include try14.constraints
// include try15.constraints
// include try16.constraints
// include try17.constraints
// include try18.constraints
// include try20.constraints
// include try22.constraints
// include try23.constraints	// BUGGY!  inconsistent Hbonds.
// include try24.constraints
// include try26a.constraints
// include try26b.constraints
// include try26c.constraints
include try28.constraints


SetCost gen6.5 0.2 wet6.5 1 dry5 3 dry6.5 12 dry8 4 dry12 1.5 \
	phobic_fit 0.5 \
	sidechain 0.2 \
	clashes 1.0 sidechain_clashes -0.2 backbone_clashes 0.5 \
	break 30  \
	pred_alpha2 1 \
	constraints 0.2 \
	contact_order 0.5

//	nonhelix_hydrogen_bonds 10
//	hydrogen_bonds 1


//	known_ssbond 0.5
//	alpha 1 alpha_prev 1 \