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


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

InFilePrefix decoys/

ReadTargetPDB T0419.try4-opt3.gromacs0.repack-nonPC.pdb
NameTarget T0419

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time

# 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 1p5z.mmol chain A name 1p5zA
ReadTemplatePDB 1p5z.mmol chain B name 1p5zB

OutFilePrefix 

InFilePrefix 1p5zB/
ReadFragmentAlignment NOFILTER T0419-1p5zB.two-domain-a2m
InFilePrefix
PrintMultimerPDB 2 try4-try4-1p5z.pdb
Time