Hi all,
I've performed molecular docking using ClusPro. One of the chain from the ligand merged to a chain from the receptor when I wanted to study the protein-protein interaction using iCn3D. Thus, I unable to study the actual interaction of the protein and ligand. How to avoid ligand and receptor protein chain from merging into one chain after molecular docking? Or is there any other software that I can try to perform docking and study the interaction of the docked proteins?
Change the ligand's or the pdb file's chain id. This may help: https://pross.weizmann.ac.il/chain-selection/. I believe the chain id is missing.
This is not common during docking process. However, some times both proteins atoms might be in chains with the same IDs(For example bot in chain A). In such case, you can edit one of the pdb file with a text editor like notepad and rewrite the A (in chain ID) in different name (B, for example).
Alireza Mohebbi Thank you for the idea, it helps. I've changed the chain ID using Pymol before docking process.
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