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


InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time


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

InFilePrefix 

 ReadTargetSeq T0500.a2m 1
 NameTarget T0500
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/



InFilePrefix decoys/

ReadConformPDB T0500.MQAY1-opt3.gromacs0.repack-nonPC.pdb	# < BAKER-ROBETTA_TS4
	# best Rosetta energy

ReadConformPDB fragment-try6-A1-P45.pdb.gz   
ReadConformPDB fragment-try6-P155-P225.pdb.gz
ReadConformPDB fragment-try6-P45-P155.pdb.gz 
ReadConformPDB fragment-try6-P225-P271.pdb.gz
ReadConformPDB fragment-try6-P271-P421.pdb.gz
ReadConformPDB fragment-try6-P421-P453.pdb.gz
ReadConformPDB fragment-try6-P453-P579.pdb.gz
ReadConformPDB fragment-try6-P579-P612.pdb.gz
ReadConformPDB fragment-try6-P612-P665.pdb.gz
ReadConformPDB fragment-try6-P665-E829.pdb.gz


Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-MQAY1-try6.pdb superpose 

# Can specify a set of atoms as optional arguments of printAllConformPDB
# to give initial set of atoms to align.
# Format: 	atom A7.CA	atom K252.CA	...

Time

quit