SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-2191.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
MakeGenericFragmentLibrary
Time

InFilePrefix ../
# If multimer is not already in pdb, but needs crystal symmetries to generate,
# then fetch the "biological unit" from pdb and use the following commands:
// ReadTemplatePDB 1xxx.pdb1 model 1 name 1xxxA
// ReadTemplatePDB 1xxx.pdb1 model 2 name 1xxxB
# Or use the PQS mmol file
ReadTemplatePDB 2ge3_1.mmol chain A name 2ge3A
ReadTemplatePDB 2ge3_1.mmol chain B name 2ge3B
Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix ../decoys/
ReadTargetPDB T0417.try6-opt3.pdb
NameTarget T0417

OutFilePrefix decoys/
InFilePrefix ../2ge3A/
ReadFragmentAlignment NOFILTER T0417-2ge3A.dimer-a2m
PrintMultimerPDB 2 dimer-try6-2ge3_1.pdb
Time


InFilePrefix ../decoys/
ReadTargetPDB T0417.try5-opt3.pdb
NameTarget T0417

OutFilePrefix decoys/
InFilePrefix ../2ge3A/
ReadFragmentAlignment NOFILTER T0417-2ge3A.dimer-a2m
PrintMultimerPDB 2 dimer-try5-2ge3_1.pdb
Time


InFilePrefix ../decoys/
ReadTargetPDB T0417.MQAU1-opt3.pdb
NameTarget T0417

OutFilePrefix decoys/
InFilePrefix ../2ge3A/
ReadFragmentAlignment NOFILTER T0417-2ge3A.dimer-a2m
PrintMultimerPDB 2 dimer-MQAU1-2ge3_1.pdb
Time


InFilePrefix ../decoys/
ReadTargetPDB T0417.try1-opt3.gromacs0.pdb
NameTarget T0417

OutFilePrefix decoys/
InFilePrefix ../2ge3A/
ReadFragmentAlignment NOFILTER T0417-2ge3A.dimer-a2m
PrintMultimerPDB 2 dimer-try1-2ge3_1.pdb
Time


InFilePrefix ../decoys/
ReadTargetPDB T0417.try3-opt3.gromacs0.repack-nonPC.pdb
NameTarget T0417

OutFilePrefix decoys/
InFilePrefix ../2ge3A/
ReadFragmentAlignment NOFILTER T0417-2ge3A.dimer-a2m
PrintMultimerPDB 2 dimer-try3-2ge3_1.pdb
Time