I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein before docking? For example, before docking, the protein has thousands of atoms, but the protein-ligand complex after docking only has dozens of atoms. I just started to study molecular docking and I really hope to get your answer, thank you!
"AutoDock writes out only the coordinates of the atoms in the ligand (and any moving parts of the receptor, if you are doing a flexible sidechain docking). It does not write out the coordinates of the fixed part of the receptor."
You would need to use the input protein structure along with the output ligand files to visualize ligand-protein complexes.
http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Analysing%20Results
"AutoDock writes out only the coordinates of the atoms in the ligand (and any moving parts of the receptor, if you are doing a flexible sidechain docking). It does not write out the coordinates of the fixed part of the receptor."
You would need to use the input protein structure along with the output ligand files to visualize ligand-protein complexes.
http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Analysing%20Results
Might be this reduction is made because otherwise, calculations will take almost infinite time. You are using dimension to describe this reduction, but in my opinion, the correct description is size reduction. However, this is something that users of docking do not tell. The whole docking calculation procedures are not very well understood, I guess. Results might be perhaps random... Can you try this randomness?
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