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 TR454.a2m 5
 NameTarget TR454
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first
InFilePrefix decoys/

ReadConformPDB TR454.try17-opt3.pdb	# < try13-opt3 < try12-opt3 < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
ReadConformPDB TR454.try13-opt3.pdb	# < try12-opt3 < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
ReadConformPDB TR454.try10-opt3.unpack.gromacs0.repack-nonPC.pdb  # <try7-opt3  < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
# ReadConformPDB TR454.try7-opt3.pdb	# < try4-opt3
# ReadConformPDB TR454.try4-opt3.pdb	# < dimer-TR454.try3-2uxu 
# ReadConformPDB dimer-TR454.try3-1pb6.pdb.gz
# ReadConformPDB dimer-TR454.try3-2uxu.pdb.gz

ReadConformPDB TR454.try16-opt3.unpack.pdb # < try15-opt3 < dimer-TR454.try14-2uxu
ReadConformPDB TR454.try15-opt3.unpack.pdb # < dimer-TR454.try14-2uxu

ReadConformPDB TR454.try9-opt3.pdb	# < try8-opt3 < dimer-TR454.try6-2uxu 
ReadConformPDB TR454.try8-opt3.pdb	# < dimer-TR454.try6-2uxu 

ReadConformPDB TR454.try19-opt3.pdb	# < dimer-try18-2uxu

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB best-models.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