The input to SMART should be either a standard MOL2-formatted file or a standard SD/MOL file (3D) containing the structure of the ligand to be docked.
ProCESS inpt file format:
ProCESS requires all input proteins (if running any of the flexible modes) to be similar mol2 files. For two proteins to be considered similar, they must have the same number of atoms, the same residue naming and have the same atoms within each residue (including atom names).
Prepare input file format:
Prepare takes a PDB file and converts it to a mol2 with hydrogens added (and more...)
