Fig. 1.

(A) Crystallographic bound structure of benzamidine and trypsin (PDB ID code 3PTB). Parameters for benzamidine were derived from the generalized Amber force field (GAFF), and restrained electrostatic potential (RESP) partial charges fitted with Gaussian. The C7 atom was used as a reference to define the reaction coordinate. (B) System setup. Trypsin (T) and benzamidine (B) are separated by a distance of 35 Å along z first, and then solvated with a TIP3P water box extending 12 Å from any atom in all directions.