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Thank you for your help.

Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or videos which shows how to do that. Actually, I want to intercalate at particular site and I did Autodock to but it shows that the ligand is not at all intercalated.

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  • $\begingroup$ As mentioned in a previous Q intercalation requires pi stacking and interactions of quadrupole moments. The Lenard-Jones potential is a poor proxy for this and you may need to use quantum mechanics —have you looked into Gaussian etc.? (I may be wrong though if there are lots of polar interactions) $\endgroup$
    – Matteo Ferla
    Commented Nov 23, 2021 at 9:18
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    $\begingroup$ Link to previous question which this may be a duplicate of: building complex drug-dna for AMBER software $\endgroup$
    – Matteo Ferla
    Commented Nov 23, 2021 at 9:18

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