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 T0437.a2m 1
 NameTarget T0437
// 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 T0437.try9-opt3.pdb
# ReadConformPDB T0437.try8-opt3.pdb	> try9
# ReadConformPDB T0437.try7-opt3.pdb	> try9
# ReadConformPDB T0437.try6-opt3.pdb	> try9

ReadConformPDB T0437.try5-opt3.pdb
# ReadConformPDB T0437.try4-opt3.gromacs0.repack-nonPC.pdb > try5

ReadConformPDB T0437.try1-opt3.repack-nonPC.pdb

ReadConformPDB T0437.try2-opt3.gromacs0.pdb

ReadConformPDB T0437.MQAU1-opt3.gromacs0.pdb

# choose one of the remaining models?

#	ReadConformPDB T0437.MQAC5-opt3.pdb	# rejected by Firas and John
# ReadConformPDB T0437.MQAU5-opt3.gromacs0.repack-nonPC.pdb
# ReadConformPDB T0437.MQAC1-opt3.gromacs0.pdb
# ReadConformPDB T0437.try3-opt3.gromacs0.repack-nonPC.pdb


InFilePrefix 
# ReadConformPDB T0437.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0437.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0437.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0437.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0437.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