A molecular structure can look ready for simulation and still contain details that complicate preparation: alternate atom locations, waters you do not intend to model, unwanted small molecules, or monatomic ions. Cleaning these up before the main GROMACS preparation workflow can make it easier to define the system you actually want to simulate.
But cleanup is not simply a matter of deleting everything that is not protein. A ligand may be central to the question you are studying, and a water molecule in an active site may have a functional role. The useful first step is to decide what belongs in the model—and only then remove what does not.
Start with a structure you can inspect
For a walkthrough, the SAMSON documentation uses the 1AKI structure. In SAMSON, load it through Home > Fetch by entering 1AKI under PDB or PDB (mmCIF), then clicking the matching Load button. Import parameters can be left at their defaults for this example. A structure already saved on your computer can instead be opened with Home > Open.
Make cleanup a set of decisions
Open Home > Prepare and consider the cleanup options in light of your simulation goal:
- Remove alternate locations. This removes alternate-position data that can make the starting structure less straightforward to prepare.
- Remove ligands only if you do not need them. A ligand you plan to simulate should stay. If you want to keep an arbitrary molecule or cofactor, remember that it may require a topology file before it can be included in a GROMACS simulation.
- Decide carefully about water. Removing all water can be convenient, but it is not appropriate for every system. Tightly bound or active-site waters may be functional and worth preserving.
- Remove monatomic ions when they are not part of the model you intend to prepare.
- Hydrogen addition is optional here. GROMACS can add hydrogens during its workflow, so this option does not have to be selected at this stage.
Keep important waters, remove distant ones
If you want to remove crystal waters outside an active site while preserving nearby waters, use a targeted selection instead of removing all water. First select structures, residues, or atoms in the active site—for example, a ligand or water molecule. Then right-click the selection in the Document view or Viewport and choose Expand selection > Advanced.
In the dialog, set the node type to Water and choose beyond a distance from the active-site selection. The documentation illustrates this with a selection of water beyond 5 Å; choose a distance appropriate to your use case rather than treating that example as a universal cutoff. Enable auto-update if you want to inspect the selection as you adjust it. Before deleting anything, verify which waters are selected. Then right-click the selection and choose Erase selection.
What if a molecule needs to stay?
For arbitrary molecules you want to include, GROMACS needs topology information. The documentation points to external tools such as the ATB Server or CGenFF for generating topology files (.itp). These files can then be provided during the GROMACS Wizard Preparation step. If you do not need a molecule and cannot generate or provide its topology, removing it during cleanup may be the simpler route.
The main principle is to make cleanup intentional: remove unwanted structural clutter, but preserve molecules that matter to the biology or to your simulation question. After this pre-processing step, continue to preparation to define the simulation model, box, solvent, ions, and project files.
Learn more in the original GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.