SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-40pc-3157.atoms

# The rotamer library need not be from the same set of chains as the TrainingAtoms.
# It encodes the most probable conformations of sidechain and backbone
# for each residue type.
ReadRotamerLibrary dunbrack-40pc-3157.rot

Time


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

InFilePrefix 

# ReadTargetPDB TR476.blank.pdb
ReadTargetSeq TR476.a2m 2
NameTarget TR476
PopConform

InFilePrefix

include costfcn-init.under
# include MQA_init.costfcn
include try3.costfcn
// Scale the break and clash costs down, then gradually back up again
ScaleCost break 0.25 soft_clashes 0.25



Time

MakeGenericFragmentLibrary
Time


InfilePrefix

Time

// Switch to the following (commenting out the TryAllAlign)
// to polish existing models
InfilePrefix decoys/
# include read-pdb.under
ReadConformPDB TR476-untrimmed.pdb.gz
ReadConformPDB TR476.pdb.gz
ReadConformPDB TR476.try2-opt3.pdb.gz
ReadConformPDB TR476.try3-opt1-scwrl.pdb.gz
ReadConformPDB TR476.try3-opt1.pdb.gz
ReadConformPDB TR476.try3-opt2.pdb.gz
ReadConformPDB TR476.try3-opt3.gromacs0.pdb.gz
ReadConformPDB TR476.try3-opt3.gromacs0.repack-nonPC.pdb.gz
ReadConformPDB TR476.try3-opt3.pdb.gz
ReadConformPDB TR476.try3-opt3.repack-nonPC.pdb.gz
ReadConformPDB from-try10.pdb.gz


CostConform
Time


InitMethodProbs \
	Backrub		5 \
	BigBackrub	3 \
	FixOmega	0.3 \
	HealPeptide	0.3 \
	JiggleSubtree	3 \
	JiggleSegment	3 \
	OptSubtree	1 \
	OptSegment	1 \
	OptAllSegments	0.3 \
	ShiftSubtree	0.3 \
	ShiftSegment	0.3 \
	TweakPhiSubtree	0.3 \
	TweakPhiSegment	0.3 \
	TweakPsiSubtree	0.3 \
	TweakPsiSegment	0.3 \
	TweakPsiPhiSubtree	0.3 \
	TweakPsiPhiSegment	0.3 \
	TweakHbondSubtree	0.3 \
	TweakHbondSegment	0.3 \
	TweakMultimer	0.3 \
	TweakPeptide	0.3 \
	OneRotamer	5 \
	ClashingRotamer	3 \
	ClusteredRotamer	3 \
	ReduceBreak	5 \
	CloseGap	5 \
	HealGap	5 \
	MoveGap	5 \
	ReduceConstraint	5 \
	ImproveSSBond	0 \
	InsertSSBond	0 \
	InsertAlignment	1 \
	InsertSpecificFragment	5 \
	InsertFragment	5 \
	TwoFragment	5 \
	CrossOver	10 \
	DoubleCross	10 \
	CrossAndInsert	5 \
	ReduceClash	5


OptConform pool_size 20 num_gen 1 gen_size 100 \
	super_iter 1 super_num_gen 100 \
	use_all keep_all

CostConform
Time

OutFilePrefix 

ExtractConformationsContacts 8 all_contacts evalue
TIME
OptimizeConstraints all_contacts align rejected noncontact TR476.t06.CB8-sep9.rdb 
TIME
PrintContacts align		conform.constraints 
PrintContacts rejected.bonus	conform_rejected_bonus.constraints
PrintContacts noncontact.bonus	conform_noncontact_bonus.constraints

# PrintContacts all_contacts all

TIME
quit