Hi, thanks, by compiling, I presume you would be referring to the .linuxgccrelease files? If yes, I did. However, in the webpage you provided, [path to executable]/docking_protocol.[platform|linux/mac][compile|gcc/ixx]release –database [path to database] @options, how do i input the pdb files to be docked? Is it okie if you give an example for this command, for the case where R.pdb is the receptor and L.pdb is the ligand? Many many thanks.! 