// 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 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 T0151.blank.pdb
NameTarget T0151
PopConform	// get rid of uneeded all-zero conformation


InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0151.t2k.alpha.rdb 2 alpha alpha_prev

// fix length of hairpin 1
Constraint	191	313	38 42.315 48	// CA A29 CA T44

// fix length of hairpin 2
Constraint	607	699	24 27.243 33	// CA R82 CA E92

// fix hairpin separation
Constraint	313	699	35 43.683 55	// CA T44 CA E92

// fix spacing from hairpin2 to short hairpin
Constraint	164	699	22 25.946 30	// CA S24 CA E92

// put in some hydrogen bonds for hairpin1
//	A29-I59	S35-L53 I39-D49
Constraint	190	446	2 2.7 3.2	// N A29	O I59
Constraint	195	440	2 2.7 3.2	// O A29	N I59

Constraint	228	413	2 2.7 3.2	// N V33	O L55
Constraint	233	407	2 2.7 3.2	// O V33	N L55

Constraint	240	394	2 2.7 3.2	// N S35	O L53
Constraint	244	388	2 2.7 3.2	// O S35	N L53

Constraint	253	381	2 2.7 3.2	// N P37	O D51
Constraint	258	374	2 2.7 3.2	// O P37	N D51

Constraint	271	368	2 2.7 3.2	// N I39	O D49
Constraint	277	362	2 2.7 3.2	// O I39	N D49

// put in some hydrogen bonds for hairpin2
// These seem to be off by 1
	// R82-V101 F88-K95 
	//Constraint	614	784	2 2.7 3.2	// N R82	O V101
	//Constraint	623	779	2 2.7 3.2	// O R82	N V101

	//Constraint	668	735	2 2.7 3.2	// N F88	O K95
	//Constraint	677	728	2 2.7 3.2	// O F88	N K95

Constraint	604	808	2 2.7 3.2	// N S80	O D104
Constraint	608	802	2 2.7 3.2	// O S80	N D104

Constraint	651	746	2 2.7 3.2	// N R86	O R96
Constraint	660	737	2 2.7 3.2	// O R86	N R96

Constraint	688	726	2 2.7 3.2	// N T90	O E94
Constraint	693	719	2 2.7 3.2	// O T90	N E94

// put in some hydrogen bonds for short hairpin
// R20-V28
Constraint	134	195	2 2.7 3.2	// N R20	O V28
Constraint	143	190	2 2.7 3.2	// O R20	N V28


// hold barrel together:
Constraint	424	770	2 2.7 3.2	// O R56	N D100

Constraint	74	238	2 2.7 3.2	// N N12	O A34

Constraint	33	604	2 2.7 3.2	// N I7		O G81


SetCost gen6.5 0.2 wet6.5 0.2 dry6.5 1.0 dry8 1.0 dry12 1 \
	phobic_fit 0.2 \
	sidechain 0.2 \
	clashes 1 sidechain_clashes -0.2 backbone_clashes 0.5 \
	break 5  \
	constraints 0.03 \
	pred_alpha2 1  \
	contact_order 1

//	known_ssbond 0.5
//	radius_norm 0 radius_fit 0.2 \