# -----------------------------------------------------------------------------
#
# In GRAMM-webserver docking, the input structures are labeled as “receptor” and
# “ligand” and the chain IDs in both molecules (receptor and ligand), are 
# labeled alphabetically starting with A in receptor proteins. 
#
# In GRAMM docking algorithm, the receptor protein is held in a fixed position,
#  while the ligand protein is rotated and translated to identify the optimal
# binding pose. The algorithm calculates the energy of the interaction in each 
# position, based on the geometric fit and energy-based scoring, and selects 
# the ligand pose with the lowest energy. The docked models are stored in PDB 
# format named model#.pdb (# = rank of the predicted model).
#
# -----------------------------------------------------------------------------
# Description of the files:
# -----------------------------------------------------------------------------
#
# receptor.pdb               :Submitted receptor PDB file
# lignd.pdb                  :Submitted ligand PDB file
# receptor-ligand_model#.pdb :receptor-ligand complex PDB file of docked models
# ligand_model#.pdb          :PDB file of docked ligand models 
# receptor-ligand.res        :Rotation angles and translation coordinates of
#                             ligand protein for scan stage docking models
# output.log                 :Out message or Error log file                              
#
# -----------------------------------------------------------------------------
#
# Send questions or comments to gramm@ku.edu
#
# -----------------------------------------------------------------------------
