Figure 7. Structures of peptides (cube representations) and a water
molecule (ball-and-stick representation).
The entire process, including 1) fragmentation, 2) generation of
Gaussian input files and job submission, and 3) results analysis, is
illustrated in Figure 8. For fragment energy calculation, we used the
B3LYP functional together with the 6-31G(d) basis. The input files were
submitted to the grid environment, and a grid node (ERA, located at the
Computer Network Information Center, CAS, China) installed with the
Gaussian 09 package was selected to execute QM
calculations.73