Script Name                     Output
    --------------------------------------------------------------------------------
 1. 01_reverseCluster.tcl           ./configurations.dat
 2. 02_viewConfigs.tcl              -
 3. combinePDBs.py                  x_together/*pdbs

      This has the PDBs of the protein and ligand combined. The ligand is not in the
      correct placement for the protein. These PDBs will be used to compare to full
      Anton trajectory to compute the transformation matrix of the proteins, then
      apply that matrix to the ligand (next step). After this move, the correctly
      positioned ligand will be written out by itself (without the incorrectly placed
      protein) in the next step.

 4. 04_centerLig.tcl                y_ligCentered/*pdbs 
 5. combinePDBs.py                  z_togetherCentered/*pdbs
 6. 06_viewAllConfigs.tcl           -