I docked a metal -coordination complex to protein. I further tried to visualize the ligand interactions using discovery studio. Upon selection, I find that the bonds of my ligand co-ordination to copper are missing. I tried even changing the charge of my copper metal from neutral to +2 state still there is no visibility of the co-ordination bonds. I presume this absence is due to ligand interactions with protein residues at the docked site. Is this true, or anything else needs to be done? Kindly help.
Hi Rahul,
1) Check your ligand structure(s) being coordination or chelate form.
2) Check partial charges of ligand atoms, being suitable for coordination or chelation.
It will be helpful if you tell what docking software you have used for this experiment.
I am also faceing same problem. The co-ordinate bond did not appear when I try to visualise in pymol and discovery studio.
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