Body: <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-28T14:08:00.280Z
Comments.Text: 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: https://www.researchgate.net/post/Pi-pi-and-cation-pi-interactions-in-force-fields
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-28T14:50:20.627Z
Comments.Text: 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.
Comments.UserDisplayName: dnalectronics
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-28T14:54:51.597Z
Comments.Text: 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.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-28T14:57:38.577Z
Comments.Text: 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!
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-29T19:26:44.487Z
Comments.Text: Thank you for your help
Comments.UserDisplayName: dnalectronics
Tags: <ngs><phylogenetics><docking><drugs><molecular-dynamics>
Title: Drug-DNA complex simulation using AMBER
ThreadText: # Drug-DNA complex simulation using AMBER
  
  (Asked by: username_0 on 2021-10-28)
  
  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.
  
  **Tags:** ngs, phylogenetics, docking, drugs, molecular-dynamics
  
  > **Comments:**
  > **username_1**: 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: https://www.researchgate.net/post/Pi-pi-and-cation-pi-interactions-in-force-fields  
  > **username_0**: 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.  
  > **username_1**: 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.  
  > **username_1**: 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!  
  > **username_0**: Thank you for your help  
  
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  ## 0 answers
  
  