my macromulecule is MHC class 1
I don't know what kind of charges (kollman or gasteiger) do I add to my receptor. My ligand is a small peptide.
Hi Heidarali,
If you are going to try AutoDock Vina, either will be OK, because Vina ignores receptor's charges for scoring.
For AutoDock 4, I recommend both. After several docking, you should carefully check your results with your experimental data.
I wonder if the FAQs (question 2) of this document would be of help: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-with-autodocktools/UsingAutoDockWithADT_v2e.pdf
kollman for macromulecule and gasteiger for ligand but since your ligand is a peptide, you should add kollman to the ligand as well.
thank you very much dear friends.
Always welcome.
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