===============================================================================
                             2. Ligand Preparation
===============================================================================

This part shows how to prepare an input file for ligand pocket with
'prepare_ligands.py' in 'scripts' directory.

Three files are required (file names in this directory is shown between []):

Ligand MOL2: ligand files to be screened. they should be prepared in MOL2
       	     format
	     [ZINC01484895.mol2, ZINC03833861.mol2]
Input file: contains input parameters
      	    [lig_prep.in]

===============================================================================
                    Description of parameters in input file
===============================================================================

PLPS_path: path of PL-PatchSurfer2 package
PDB2PQR_path: path of PDB2PQR is installed
APBS_path: path of APBS is installed
BABEL_path: path of openbabel is installed
XLOGP3_path: path of XlogP3 is installed
OMEGA_path: path of OMEGA is installed
n_conf: number of maximum conformations to be generated for each ligand
ligand_file: ligand MOL2 file names

===============================================================================
                                Runnung Scripts
===============================================================================

Type in command window as below:
$python ../../scripts/prepare_ligands.py lig_prep.in

===============================================================================
                                  Output file
===============================================================================

After finishing running scripts, folders with the ligand name will be
generated. Each directory contains the conformations from OMEGA in PDB format
and SSIC files generated from the conformations 

===============================================================================
                           Visualizing seed position
===============================================================================

To see the seed position (center of patch) with molecule structure, generate
PDB file by using 'convert_ssic_to_pdb.py' as below:
$python ../../scripts/convert_ssic_to_pdb.py [SSIC file] [output PDB file]

===============================================================================
