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 T0440.a2m 1
 NameTarget T0440
// 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/
// include read-pdb.under
ReadConformPDB T0440.try9-opt3.pdb	# < dimer/try7-opt3 < try5-opt3 < MQAC1-opt3.gromacs0
ReadConformPDB T0440.try8-opt3.gromacs0.repack-nonPC.pdb	# < dimer/try6-opt3 < try4-opt3< try2-opt3 < try1-opt3 < align(2yxoA)

ReadConformPDB T0440.try10-opt3.gromacs0.repack-nonPC.pdb	# < MULTICOM-REFINE_TS5

ReadConformPDB T0440.try5-opt3.pdb	# < MQAC1-opt3.gromacs0
# ReadConformPDB T0440.try4-opt3.pdb	# < try2-opt3 < try1-opt3 < align(2yxoA)
# ReadConformPDB T0440.try2-opt3.gromacs0.repack-nonPC.pdb # > try4
# ReadConformPDB T0440.MQAC1-opt3.gromacs0.pdb	# < Zhang-Server_TS4 # > try5
ReadConformPDB T0440.MQAU1-opt3.gromacs0.pdb	# < Zhang-Server_TS4 

# ReadConformPDB servers/YASARA_TS1

InFilePrefix 
# ReadConformPDB T0440.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0440.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0440.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0440.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0440.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices

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