"prot:A:MET1:HN1 and prot:A:MET1:HN1 have the same coordinates" Error While Performing Flexible Docking?

I wanted to perform the flexible docking using AutoDock Vina on Window 11. However, when I had selected the flexible residues and clicked "choose torsion in currently selected residues", it crashed. What's wrong with it? - _ -

I have been trying to dock a certain protein with nd ion i downloaded from rcsb but after i add it to pyrx and try to convert it to ligand i get the following error. I tried converting the sdf file to pdb using pymol, chimeraX, avogadro, open babel but even then when i open the file it gives me this error: ligand: :UNK0:Nd and ligand: :UNK0:Nd have the same coordinates. Could someone please help?

Update: I want to dock an unbound protein with the neodymium metal ion which i downloaded from rcsb in sdf format and later tried to convert it to pdb using the aforementioned softwares for autodock to accept it but i can't get it to be accepted by autodock as a proper ligand. Apparently I am unable to get any of the rare earth elements to be accepted properly as ligands.

i am docking ligand against urease enzyme PDB:ID 3la4. active pocket contains Ni atoms. but during process software gives error of adding parameters of Ni first.

how to add these parameters and save file?

i have one protein with two different active sites and normally hydrolyzed by two different chemical compounds in the human body in normal condition.

so question is that can i dock this with two analogy of normal compounds by using Audodock 4.2

Please help me to generate ligand topology for the file attached here.

I am actively seeking a PhD position in Chemistry at a renowned university in the United States, Germany, Canada, or Switzerland. My research expertise is focused on organic chemistry, photoluminescent materials, and stimuli-responsive materials. I hold a Master's degree in Chemistry from National Taiwan University (NTU), where I achieved high GPAs in both my Bachelor's and Master's programs. Moreover, I am passionate about advancing research in these fields and am eager to contribute to innovative projects. Therefore, if my background aligns with your research interests, I would be happy to discuss potential opportunities further.