recommendations:
1. in a working directory:
  have three directories of data:

    centers/   whatever is in here, have a yaml file with a set of centers
               corresponding to each receptor or set of receptors. Copy and paste
               from this yaml into the configuration file.
               scripts: 
                1. FTMAP scripts for processing those pdbs
                2. center_gen.pl center_append.pl to generate summary YAML

    receptors/ pdbqt files for receiving molecule of interest 
               scripts:
                generate using MGLTools

    ligands/   sets of json files generated from big db of pdbqt files  
               scripts: setup_ligands_sets_mce.pl
               MGLTools for initial db of pdbqt files.  I have a ~/db directory 
               with a couple of sets (NCI_diversityset2 and a ZINC subset).

  and then directories for work and analysis
    docking_NCI/
    docking_ZINC/
    etc.
  
    Within the working directory, copy the broadcast.pl script over and the example.yaml 
    configuration file. Adjust conf file: the first screen or dock should pull from the 
    ligands/ databases (data: path/to/ligands), but write to local databases (in new 
    scratch dirs). the next screens can read and write to the same scratch directory (now 
    also data). Invoking broadcast.pl will apply the configuration file across all json
    files loaded from the data directory and invoke ligands_dock.pl.  After accumulating 
    docking data, separate good from bad, analyze etc.
  
    see descriptions in example.yaml and ligands_dock.pl.

