<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>

CC BY-SA 4.0
2021-10-28T14:08:00.280Z
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
Matteo Ferla
CC BY-SA 4.0
2021-10-28T14:50:20.627Z
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.
dnalectronics
CC BY-SA 4.0
2021-10-28T14:54:51.597Z
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.
Matteo Ferla
CC BY-SA 4.0
2021-10-28T14:57:38.577Z
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!
Matteo Ferla
CC BY-SA 4.0
2021-10-29T19:26:44.487Z
Thank you for your help
dnalectronics
<ngs><phylogenetics><docking><drugs><molecular-dynamics>
Drug-DNA complex simulation using AMBER
# 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

