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/
ReadConformPDB TR429.try4-opt3.gromacs0.pdb	# < chimera-N3-try3

InFilePrefix  R100-P176/decoys/
ReadConformPDB TR429.try4-opt3.gromacs0.pdb name C-try4	# < R100-P176/try1-opt3

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-chimera-try4-C4.pdb superpose \
	residue Y149 residue A150 residue V153 residue C162 residue F166 \
	residue D133 residue E135 residue S137 residue N151 residue G155