When I visualize the docked fragments during a run it shows that the docked fragments are outside the protein (not in the binding pocket) when viewed with chimera. To visualize, I am using the PDB structure then opening the SDF file with Chimera. I am sure the coordinates I used for docking are correct. I used the Webina server to find the coordinates as well as Chimera and they were the same.
How am I able to visualize the binding mode after a run?
Hi Brandon. Much thanks for your interest in AutoGrow4. Without seeing your files, I can’t say for certain what the problem is. But for what it’s worth, I don’t think the SDF files contain the docked compounds. If I’m not mistaken, the docked poses end in ".pdbqt.vina" and are PDBQT formatted. I hope this helps. ~Jacob
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