Preparing a receptor for a molecular docking simulation can sometimes feel more complex than the docking itself. Whether you’re working on a protein-ligand system or trying to simulate docking into DNA or RNA, the setup process can be a source of frustration—especially when you have to juggle multiple tools or manually edit structural data.
If you’re using SAMSON, there’s a way to simplify and streamline this step using the FITTED Suite Extension developed with Molecular Forecaster. This integrated approach not only speeds up your workflow but also reduces the likelihood of setup errors.
Why receptor setup matters
A poorly prepared receptor can easily undermine the reliability of docking results. Residues might be mispositioned, water molecules could be wrongly positioned, or essential hydrogens may be missing. SAMSON helps automate many of these steps, but it’s still useful to know how to properly select and define your receptor structure before running simulations.
Step-by-step: Setting up your receptor
Once you launch SAMSON and load your molecular structure (e.g., 1E2K-A.sam from the tutorial archive), you’ll see your protein structure appear in the Document view. Here’s how to configure your receptor:
- Select your protein model. In the Document view, locate the structural model corresponding to your target protein—in this tutorial, that’s
1E2K. Click to select it. - Open the FITTED Suite App: Navigate to Home > Apps > Biology or search for “FITTED Suite” using the Find everything… search box at the top.
- Set the receptor. In the FITTED interface, find the “Set receptor” section and select “From document”. Then click Set.
- Check water and macromolecule parameters. By default, the extension will treat the structure as a protein, and water molecules are managed automatically. If your receptor is a metalloprotein, DNA, or RNA, be sure to update the “Macromolecules” parameter accordingly.
Optional cleanup — Minimal effort
For the provided tutorial system, no editing is required. The FITTED Suite’s built-in PREPARE tool takes care of common liabilities, such as adding hydrogens and generating possible tautomers.
However, if you’re working with your own PDB file, it’s a good idea to verify that:
- Atoms don’t have alternate conformations.
- Missing residues or atoms are addressed.
- The water network is optimized.
You can initiate these preparations via Home > Prepare.
Final thoughts
This streamlined approach helps eliminate one of the most common bottlenecks in modeling: receptor setup. It’s especially helpful in educational or high-throughput environments where speed and reproducibility are important. Once the receptor is set, you can quickly move on to defining the binding site and ligand, and then perform your docking calculations with confidence.
To read the full tutorial and see how to continue with ligand and binding site setup, visit the FITTED Suite documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.