- I am interested in studying the binding conformations of an organic ligand with an organometallic complex bearing a Cu2+ metal center. While I found numerous tutorials on protein-ligand docking, I couldn't locate any that specifically address my area of interest, leaving me to question whether this approach is feasible.
- Following the standard protein-ligand docking protocol, I attempted to dock the ligand to the metal complex (generated through Gaussian and optimized using the MCPB.py program in Amber) using Autodock 4.2. I proceeded by treating the target complex as the 'macromolecule' and preserving its original charges instead of applying Kollmann or Gasteiger charges, and I completed the docking process. However, upon analyzing the resultant files, I became doubtful of the outcomes as all the docked poses exhibited highly positive binding energies, despite MD simulations indicating stable complexes. I would greatly appreciate any guidance or potential mistakes I may have made.
Kyle A. Grice
If it's small enough, you should do DFT! Metal-ligand interactions aren't well done with most docking software. Even semi-empirical methods get metals wrong. See for example: Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy | Journal of Chemical Theory and Computation (acs.org))
Article Application of Semiempirical Methods to Transition Metal Com...
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