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I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will truly appreciate if anyone could guide me how to place my drug at the desired location in the DNA sequence using Amber.

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  • $\begingroup$ If it is only one... Can you not place it by dragging it in PyMOL? Also do check out this discussion thread about the issue of aromatic dipole moments and forcefields: researchgate.net/post/… $\endgroup$
    – Matteo Ferla
    Commented Oct 28, 2021 at 14:08
  • $\begingroup$ Thank you so much for your reply. I can try that. However, I want to know how can I know different base pairs in pymol. When I load the pdb file of my DNA sequence the base pairs cartoon all look same. Do you have any recommendations for teh software I can use to load my DNA and ligand pdb file and insert it into specific sequence and then save file as pdb may be. $\endgroup$
    – dnalectronics
    Commented Oct 28, 2021 at 14:50
  • $\begingroup$ PyMOL shows everything as cartoon by default, but you can show them as licorice. Say show sticks, polymer.nucleic. There are a few other representations possible —cf. right hand side panel under (S) for show. $\endgroup$
    – Matteo Ferla
    Commented Oct 28, 2021 at 14:54
  • $\begingroup$ I should mention, to drag stuff, click on 3-button viewing on the right hand side panel making "editing", shift+wheel button ought to be Move object. Make sure to save often as there's no undo! $\endgroup$
    – Matteo Ferla
    Commented Oct 28, 2021 at 14:57
  • $\begingroup$ Thank you for your help $\endgroup$
    – dnalectronics
    Commented Oct 29, 2021 at 19:26

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