// 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 T0129.blank.pdb
NameTarget T0129
PopConform	// get rid of uneeded all-zero conformation

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0129.t2k.alpha.rdb 2 alpha alpha_prev


// include try30-constraints
// Include try31-constraints
//include try42.constraints

// helix-length constraints only
// include try44-constraints

// Try with and without the disulphide
// ssbond 33 135

// favor long helices by upping dry6.5 and alpha values
//SetCost gen6.5 0.2 wet6.5 0.2 dry5 1 dry6.5 4 dry8 2 dry12 1 \
//	phobic_fit 0.7 \
//	sidechain 0.2 \
//	clashes 1 sidechain_clashes -0.2 backbone_clashes 2 \
//	break 5  \
//	constraints 0.05 \
//	pred_alpha2 1 \
//	contact_order 1 \
//	known_ssbond 0.01



// favor long helices by upping dry6.5 and alpha values
// parameters set for polishing
SetCost gen6.5 0.2 wet6.5 3 dry5 2 dry6.5 14 dry8 4 dry12 2 \
	phobic_fit 0.7 \
	sidechain 0.2 \
	clashes 1.5 sidechain_clashes -0.2 backbone_clashes 0.5 \
	break 40  \
	constraints 0.03 \
	pred_alpha2 1 \
	contact_order 1 \
//	known_ssbond 0.01


//n	radius_norm 0 radius_fit 0.2 \