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 TR429.a2m 22
 NameTarget TR429
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/



InFilePrefix decoys/

InFilePrefix  E22-A101/decoys/
ReadConformPDB TR429.try3-opt3.pdb name N-try3 # < chimera-try1-init
InFilePrefix  decoys/
ReadConformPDB TR429.try3-opt3.gromacs0.pdb	# < chimera-try1-C1

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-chimera-N3-try3.pdb superpose \
 	residue Y33 residue A36 residue D38 residue A43 residue Q48 \
	residue I76 residue Y77 residue K80 residue V89 residue N93