SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
 ReadTrainingAtoms monomeric-50pc.atoms
 ReadRotamerLibrary dunbrack-2191.rot

Time


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

InFilePrefix ../TR462/

 ReadTargetSeq TR462.a2m 1
 NameTarget TR462
// Now have a random conformation---use PopConform if you don't want it.
 PopConform

Include costfcn-init.under
Include everything.costfcn
Time

OutfilePrefix decoys/

InFilePrefix ../TR462/decoys/
ReadConformPDB	TR462.pdb
SaveConformAsReal
InFilePrefix 

SetRealCost real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \
	real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \
	knot 10 clens 200  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0.2

InFilePrefix ../T0462/decoys/
include read-servers.under
include read-pdb.under

InFilePrefix ../T0462/M1-A83/decoys/
ReadConformPDB T0462.try1-init.pdb.gz name M1-A83/T0462.try1-init
ReadConformPDB T0462.try1-opt1-scwrl.pdb.gz name M1-A83/T0462.try1-opt1-scwrl
ReadConformPDB T0462.try1-opt1.pdb.gz name M1-A83/T0462.try1-opt1
ReadConformPDB T0462.try1-opt2.pdb.gz name M1-A83/T0462.try1-opt2
ReadConformPDB T0462.try1-opt3.gromacs0.pdb.gz name M1-A83/T0462.try1-opt3.gromacs0
ReadConformPDB T0462.try1-opt3.gromacs0.repack-nonPC.pdb.gz name M1-A83/T0462.try1-opt3.gromacs0.repack-nonPC
ReadConformPDB T0462.try1-opt3.pdb.gz name M1-A83/T0462.try1-opt3
ReadConformPDB T0462.try1-opt3.repack-nonPC.pdb.gz name M1-A83/T0462.try1-opt3.repack-nonPC

InFilePrefix ../T0462/G75-K154/decoys/
ReadConformPDB T0462.try1-init.pdb.gz name G75-K154/T0462.try1-init
ReadConformPDB T0462.try1-opt1-scwrl.pdb.gz name G75-K154/T0462.try1-opt1-scwrl
ReadConformPDB T0462.try1-opt1.pdb.gz name G75-K154/T0462.try1-opt1
ReadConformPDB T0462.try1-opt2.pdb.gz name G75-K154/T0462.try1-opt2
ReadConformPDB T0462.try1-opt3.gromacs0.pdb.gz name G75-K154/T0462.try1-opt3.gromacs0
ReadConformPDB T0462.try1-opt3.gromacs0.repack-nonPC.pdb.gz name G75-K154/T0462.try1-opt3.gromacs0.repack-nonPC
ReadConformPDB T0462.try1-opt3.pdb.gz name G75-K154/T0462.try1-opt3
ReadConformPDB T0462.try1-opt3.repack-nonPC.pdb.gz name G75-K154/T0462.try1-opt3.repack-nonPC

Time




OutFilePrefix
ReportCost TR462-compare.rdb
CostConform


Time

quit