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 

Time

InFilePrefix dimer/decoys/
ReadTargetPDB T0373.try1-opt2.unpack.pdb chain A
 NameTarget T0373

Time

OutFilePrefix dimer/decoys/

InFilePrefix 2a61A/
ReadFragmentAlignment NOFILTER T0373-2a61A.dimer-a2m force_alignment
PrintMultimerPDB 2 dimer-1-2a61A.pdb

InFilePrefix 2fbhA/
ReadTemplatePDB 2fbh.mmol chain A name 2fbhA
ReadTemplatePDB 2fbh.mmol chain B name 2fbhB
ReadFragmentAlignment NOFILTER T0373-2fbhA.dimer-a2m force_alignment
PrintMultimerPDB 2 dimer-1-2fbhA.pdb

InFilePrefix 1lnwA/
ReadFragmentAlignment NOFILTER T0373-1lnwA.dimer-a2m force_alignment
PrintMultimerPDB 2 dimer-1-1lnwA.pdb

InFilePrefix 1jgsA/
ReadTemplatePDB 1jgs.mmol chain A name 1jgsA
ReadTemplatePDB 1jgs.mmol chain B name 1jgsB
ReadFragmentAlignment NOFILTER T0373-1jgsA.dimer-a2m force_alignment
PrintMultimerPDB 2 dimer-1-1jgsA.pdb


Time

quit