Body: <p>Thank you for your help.</p>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-23T09:18:41.847Z
Comments.Text: As mentioned in a [previous Q](https://bioinformatics.stackexchange.com/questions/17988/building-complex-drug-dna-for-amber-software) intercalation requires pi stacking and interactions of quadrupole moments. The [Lenard-Jones potential](https://en.wikipedia.org/wiki/Lennard-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)
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-23T09:18:57.810Z
Comments.Text: Link to previous question which this may be a duplicate of: [building complex drug-dna for AMBER software](https://bioinformatics.stackexchange.com/questions/17988/building-complex-drug-dna-for-amber-software)
Comments.UserDisplayName: Matteo Ferla
Tags: <phylogenetics><docking><drugs><gromacs><molecular-dynamics>
Title: Generating intercalation site in DNA for custom sequence
ThreadText: # Generating intercalation site in DNA for custom sequence
  
  (Asked by: username_0 on 2021-11-22)
  
  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.
  
  **Tags:** phylogenetics, docking, drugs, gromacs, molecular-dynamics
  
  > **Comments:**
  > **username_1**: As mentioned in a [previous Q](https://bioinformatics.stackexchange.com/questions/17988/building-complex-drug-dna-for-amber-software) intercalation requires pi stacking and interactions of quadrupole moments. The [Lenard-Jones potential](https://en.wikipedia.org/wiki/Lennard-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)  
  > **username_1**: Link to previous question which this may be a duplicate of: [building complex drug-dna for AMBER software](https://bioinformatics.stackexchange.com/questions/17988/building-complex-drug-dna-for-amber-software)  
  
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  ## 0 answers
  
  