The Chimera charge calculation with Antechamber is not meant for organometallic molecules. It only handles most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html> Also, as far as I know, Autodock Vina is not meant to handle that type of ligand, but you could ask on the Autodock Vina mailing list to be sure. (We are not the Autodock Vina developers.) <https://vina.scripps.edu/> <https://vina.scripps.edu/questions/> Therefore, you may need to use some other program(s) for this purpose. I don't have any specific recommendations, sorry. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 20, 2024, at 1:22 PM, furkan calapoğlu via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

How can i do organometalic ligand and protein docking ?