// 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 T0141.blank.pdb
NameTarget T0141
PopConform	// get rid of uneeded all-zero conformation

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0141.t2k.alpha.rdb 2 alpha alpha_prev


// hbonds to keep V72-C76 in sheet
constraint 563	886	2.3 2.7 3.2	//  V72.O-S112.N
constraint 571	890	2.3 2.7 3.2	//  A74.N-S112.O 
constraint 574	900	2.3 2.7 3.2	//  A74.O-G114.N
constraint 586	902	2.3 2.7 3.2	//  C76.N-G114.O

constraint 576	685	2.3 2.7 3.2	//  H75.N Y87.O
constraint 584	675	2.3 2.7 3.2	//  H75.O Y87.N
constraint 592	664	2.3 2.7 3.2	//  L77.N V85.O
constraint 598	659	2.3 2.7 3.2	//  L77.O V85.N

// just off end of strands
constraint 567	696	4 6 9		// S73.CB P89.CB
constraint 573	689	4 6 7		// A74.CB V88.CB
constraint 549	869	4 6 9		// R71.CB D110.CB



SetCost gen6.5 0.2 wet6.5 0.2 dry5 2 dry6.5 14 dry8 5 dry12 1 \
	phobic_fit 0.7 \
	sidechain 0.2 \
	clashes 3 sidechain_clashes -0.2 backbone_clashes 2 \
	break 15  \
	pred_alpha2 1 \
	constraints 0.1 \
	contact_order 1

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