InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
ReadVDW initial.radii
ReadWetSpot dunbrack-925-wet-6.5.spot
ReadWetHist  smoothed-dunbrack-925-wet-6.5.hist
ReadDrySpot dunbrack-925-dry-12.spot
ReadDryHist  smoothed-dunbrack-925-dry-12.hist
SetCosts

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-925.atoms.gz
MakeGenericFragmentLibrary
ReadRotamerLibrary dunbrack-925.rot


SetScoreParam	\
	clash_penalty 4.0 wet_spot_weight 0.70 dry_spot_weight 4.0  \
	ss_bond_bonus 50.0 chain_break_penalty 5.0

InFilePrefix
ReadTargetSeq ../T0111.seq

ReportScore t111-6.5-12+rot.rdb

NameConform t111-rand

ReadFragments T0111-2oneA-karplus.index


# pick previous conformation with smallest breaks.
# on the theory that clash reduction is easier than closing breaks.
ReadConformPDB try2/t111-2oneA.2.10.pdb
NameConform t111-2oneA

SCWRLConform
 NameConform t111-2oneA-scwrl
 PrintConformPDB t111-2oneA-scwrl.pdb wet - dry -

ScoreConform

 NameConform t111-opt
 OptConform pool_size 50 num_gen 10 gen_size 200 super_iter 10  pdb
 PrintConformPDB t111-opt.pdb wet - dry -

SCWRLConform
 NameConform t111-opt-scwrl
 PrintConformPDB t111-opt-scwrl.pdb wet - dry -

ScoreConform

quit