Dear UCSF Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea. I'm inquiring about a problem in the process of making a pdbqt file during the research project. First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed. As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking. I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux. Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3)