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Article ID: 915 - Last Modified:

Can I dock a ligand that contains a Cu2+ ion?

Yes, you can run docking calculations on Cu2+ with the OPLS_2005 force field. Glide has not been parametrized with such metal-containing ligands, so you should carefully evaluate the results for validity.

When you prepare the ligand, you must change the bonds to the ligand to zero-order bonds, then assign formal charges to the metal and the atoms that were bonded to it to represent it as an ionic bond, rather than a covalent bond.

From Suite 2011 on, you can run this calculation from the Ligand Docking panel. For earlier suites, you must write out the input file, then add the following line to set the force field:

FORCEFIELD OPLS2005

Then you can run the job from the command line with $SCHRODINGER/glide.

Keywords: Glide, metal-containing ligand

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