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