Directory Structure

<run directory>
     ligands
     receptors
     dockings
     optprep
     optimized
     analysis

ligands   - a directory containing .mol2 files of the ligands to be
            screened 

receptors - a direcotry for the receptors against which to dock the
            ligands There will be one subdirectory for each receptor
            in which the receptor .pdbqt files and the .map files will
            be stored.

dockings  - a directory containing the results of individual docking
            runs for the ligands

optprep   - a directory containing the MOPAC input files for
            reoptimization using MOZYME

optimized - a directory containing the MOPAC optimized structures

analysis  - a directory containing analyses of both the docking and
            semiempircal results