Prepare is used for the protein preparation and it outputs the protein and the ligand in mol2 format.
Prepare (Protein Rotamer Elaboration and Protonation based on Accurate Residue Energy) has been developed specifically to carefully prepare all-atom protein files from PDB files (PDB_to_mol2). In this step, hydrogens are added to the protein (and water molecules) and tautomers and rotamers are generated. The complex is then optimized for optimal H-bonding. The program also allows the automated preparation of the protein input structures the flexible protein docking mode with FITTED (Make_Similar). Deletion and mutation are then carried out to ensure that all of the structures differ only by the Cartesian coordinates (i.e., conformations).
