When a drug intercalated to the DNA base pair, I expect a % of drug's surface area are overlapped with the flanking base pairs.

I tried to calculate the solvent accessible surface area of the drug with "open" and "close" option. I expect the close option give a smaller surface area, as most of the surface area should be covered by the DNA and no longer solvent accessible.

However, both option give the same results, and a closed solvent accessible surface area was observed even a "open" option was used. Why? Pls help.