I docked the ligand with the molecule by smina, and got a file in mol format. However, two object ligands and protein are needed when the program is called. The mol file generated by smina has only one object, the compound structure after the docking of protein and ligand. What should I do?
Annemarie Honegger
Did you try to combine the docked ligand with the original protein structure - I would assume that the protein coordinates are not changed by the docking process.
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