When trying to launch a Glide Grid Generation job, I see a pop-up warning indicating that "The Workspace contains one or more unidentified ligand-sized molecules". What does this mean?

This warning means that Maestro has detected at least one ligand-sized molecule that wasn't picked as the ligand in the Receptor tab of the Receptor Grid Generation panel. It is issued so you can make sure that you aren't inadvertently leaving a copy of the native ligand in the active site, where it would block the docking of other ligands. The native ligand should be picked so it can be removed from the structure, even if the grid center is set by choosing something other than the "Centroid of Workspace ligand" option in the Site tab.

Often, this warning occurs when the ligand has been picked, but the receptor structure includes cofactors or multiple chains with additional ligand molecules in other active sites. In these cases, the warnings can be safely ignored.

If the ligand in the active site is not picked it is treated as part of the rigid receptor structure. If the intention is to dock ligands into the active site next to the native ligand (for example, because the native 'ligand' is a cofactor), then it might be appropriate to leave the native ligand unpicked. In this case the warning can also be ignored.

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