Hi, I want to simulate two seperate peptids in one box. However, when I use pdb2gmx to build the top file of this system, I found that gromacs thought there is only one peptide because it added bond, angle and other energy terms between the termius of these two peptides. Is there any way to prevent this problem, or I need to change the top file by hand? Thanks a lot. Sincerely, Qian
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