Covalent docking has an extra setup challenge: the ligand is not simply finding a pocket. The workflow also needs to know which protein residue forms the covalent attachment—and, when relevant, how the ligand’s reactive atoms are represented. A bond-order or preparation choice made before docking can therefore affect what you ask the calculation to do.
This walkthrough focuses on a practical example from the FITTED Suite tutorial: docking the covalently bound ligand 7KH in the human cathepsin L structure 5MAJ. It highlights the decisions that are easy to overlook when setting up a covalent docking run in SAMSON.
Start with the bound complex
Open 5MAJ.sam from the FITTED tutorial archive. This example contains cathepsin L and the ligand 7KH 301 already bound in the structure. Using the bound ligand to define the binding site makes this a self-docking setup: the known ligand provides a reference for where the search should take place.
Open the FITTED Suite from Home > Apps > Biology. Set the 5MAJ structural model as the receptor, leaving the water and macromolecule settings at their defaults for this protein example. For the binding site, select From bound ligand, select 7KH 301, and click Set. Then set the same ligand as the docking ligand using From document.
When a bound ligand is unavailable, the binding site can instead be defined from a selection or from a position in the Viewport. The key is to make the receptor, ligand, and search region explicit before starting the run.
Preserve the ligand’s intended chemistry
In the 5MAJ tutorial example, the ligand’s nitrile group needs specific representation. The C8–N7 bond is set to a triple bond, and atoms C8 and N7 are assigned SP hybridization. The example file already has these changes, but the tutorial explains how to make them in SAMSON using Edit > Edit bonds or the Inspector.
After setting the ligand in FITTED, uncheck the option to prepare it. In this example, ligand preparation means perceiving bond order and adding hydrogens. Since the bond order and hybridization have been deliberately adjusted, leaving that option enabled could overwrite the preparation you just made. This is a useful checkpoint: if you have manually edited a ligand’s chemistry, confirm that the next step will not automatically re-prepare it.
Specify the covalent partner
Choose Covalent only as the docking mode. The tutorial uses two runs and allows you to import only the best pose if that is what you want to inspect. Next, specify the covalent residue: in this complex, the ligand binds to the sulfur atom, SG, of CYS 25 in chain A. Select the residue—or an atom within it—and click Set for Covalent residue.
A basic atom is optional. The tutorial selects ND1 in the adjacent HIS 163 residue and sets it as the basic atom. If you use this parameter, make sure the selected atom belongs to the intended adjacent residue; it is not the covalent attachment atom itself.
Run, then check what was imported
Choose an output folder if needed, then click Dock. The app reports the current stage on the button and displays logs below the results table. When the calculation finishes, results appear in the table and are loaded into the document. Selecting a result row also selects its corresponding pose, and the table can be exported as CSV.
For covalent docking, the resulting pose includes part of the residue to which the ligand is docked. In this example, the processed receptor is named 5MAJ_pro. Hide the initial structure—and its labels if they are visible—to make the result easier to inspect. The tutorial adds a Ribbons visual model for the processed receptor; zooming in on the ligand helps reveal its connection to the sulfur of CYS 25.
These checks help catch common setup mismatches before interpreting a pose: confirm the reactive ligand representation, avoid unintended ligand re-preparation, select the correct covalent residue, and inspect the imported complex in context. For the full workflow and additional analysis options, see the FITTED Suite tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.