GROMACS modification: Yes/No
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I am simulating a ligand binding to a Metalloprotein using GROMACS, after 100 ns of simulation, my ligand is quite close to the metal ion and in about 2.5 Angstrom distance. Given that the ion is active in clevaging the protein substrate’s internal bond, therefore, do I need to use QM/MM method to see if it will form a bond and the ligand internal bond will be broken?
Is it possible to see this bond formation with gromacs?
Bonds cannot break or form using classical modeling. If you want to study that, you need QM/MM.
Thank you very much,