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Hi. I want to convert ~4000 ligands in .sdf files into .pdb or .pdbqt format for molecular docking. I used " >obabel *.sdf -opdb -m " command but the structure of the ligands deformed. attached is the picture of one of the ligand after conversion to pdb. is there any reason for this? any solutions or alternatives to convert the ligands simultaneo[/img]usly without changing the structure?
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