Thank you @Iamkaant, right now I have managed to create a gold nanoparticle (sphere of pure gold, 2 nm in diamter). What I am asking is: how can I cover the surface of my gold nanoparticle with organic molecules?
I see you have suggested that I do it manually, but I haven’t been able to open the .cif file of the nanoparticle in Avogadro. Also, even if I could, wouldn’t there be a better way to cover the surface than doing it manually? Doing it manually would be extremely time consuming and tedious, so I would much rather avoid it.