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.
Hello Piyush. I am not able to completely understand your problem. Did you download a protein with an ion "nd" that you want to re-dock with using pyrx? Or did you separately download the ion file and want to perform docking with the unbound protein? Please elaborate.
Piyush Kumar I haven't personally performed metal-ion protein docking hence did not much about it, but I was able to search your query and came across this answer by Rudy J Richardson:
https://www.researchgate.net/post/Can-I-perform-Metal-ion-protein-docking/1
Hope, this may help you.
convert your file using pymol -export molecule, save it with nd.pdb
Pallavi Agrawal Thanks for your response but its not that i can't convert it to pdb, its that after i convert it to pdb using any of the softwares i mentioned in my question, and then when i try to use autodock or pyrx to convert it to pdbqt it gives the error i stated. If i try to use avogadro to get a pdbqt file directly I can't get it to be accepted as a ligand file in either autodock or pyrx.
Alvea Tasneem thank you for your response but apparently I have already gone through it and it didn't work.
Piyush Kumar Have you tried online platform for metal ion-protein docking?
Alvea Tasneem I looked some up but none of them allowed me dock the protein with lanthanides
Hey!!
Try using this server MIB2 : Metal Ion-Binding site prediction and modeling server (http://combio.life.nctu.edu.tw/MIB2/)
Submit your protein PDB ID/structure and the metal ion you want to dock. The result file can be open through Pymol, Chimera etc.
Hope this helps
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