Knowledge Base

Why does Covalent Docking quickly fail with an 'mmct_ct_extract_atoms' error?

A Monitor panel (i.e., log file) error like this:

Error: mmct_ct_extract_atoms returned error code -4 (MMCT_ERROR) for arguments (34, Bitset(61)). See the mmerr log (stderr by default) for messages from the mmlibs.

usually means an attachment residue has been specified that is missing from the input receptor structure. This can happen if the "Centroid of Workspace ligand" option for setting the grid center was chosen, and then the receptor attachment residue was picked as the ligand. The "ligand" picked with this option is removed from the receptor structure when the job is run, in order to make room for other ligands that will be docked. If there is no co-crystallized ligand and the goal is to center the grid at the attachment residue, use the "Centroid of selected residues" option instead of "Centroid of Workspace ligand", and then select residues to define the centroid.

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