Article ID: 1408 - Last Modified: April 19, 2011
How do I include a ligand in the QSite QM region if it is bound to a protein?
If you are using hydrogen caps to define the QM region, simply insert the caps in the appropriate places.
If you are using cuts and the ligand of interest is bound to a side chain, change the residue name, residue number, and chain name of the ligand to match the residue to which it is attached. To include the side chain and ligand in the QM region, use the picking tools to pick the residue side chain. The ligand will be included in the QM region even though it is not highlighted in Maestro. If the whole residue is included in the QM region via backbone picking, the attached ligand will be included also.
If the ligand is bound to a protein backbone instead of a sidechain, follow the procedure outlined above, but select the residues by backbone picking rather than side chain picking. Note, however, that the backbone cuts cannot be made within two bonds of the protein atom to which the ligand is attached.
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