A molecular structure can look ready for simulation and still contain details that complicate preparation: alternate atom locations, waters you do not need, small molecules without topology parameters, or monatomic ions left over from the structure. Removing everything that looks extra is not a safe shortcut, though. A ligand may be central to the study, and a water molecule may be functionally important.
The goal of pre-processing is not to make a structure as small as possible. It is to make a deliberate, reviewable choice about what should enter the simulation workflow—and to avoid discovering late in preparation that something important was removed or something unsupported was kept.
Start with a cleanup checklist
In SAMSON, load your structure and open Home > Prepare. For a straightforward protein-only system, consider these cleanup steps:
- Remove alternate locations. Structural files can contain alternative positions for atoms. Keeping these alternatives may create ambiguity in the starting model.
- Review small molecules before removing them. The Remove ligands option can remove molecules you do not intend to simulate. Do not use it blindly: retain any ligand or cofactor that belongs in your model.
- Decide carefully about water. Removing all water can be appropriate for some workflows, but it is not universal. Waters may be tightly bound or participate in an active site.
- Remove monatomic ions if they are not needed. Whether an ion belongs in the final system depends on your model and the subsequent preparation workflow.
- Choose whether to add hydrogens now. This is optional here, since GROMACS can also add hydrogens later.
Keep functional waters; remove distant ones selectively
“Remove water” is a convenient broad cleanup option, but it can remove waters that matter to the system. If you want to preserve active-site or tightly bound waters, select a structure, residue, or atom near the active site first. 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 waters beyond a distance from the selected site. The documentation illustrates a 5 Å example; treat the distance as a selection criterion to review, not as a universal rule. If available, use auto-update to preview the selection, then verify which waters are highlighted before erasing them.
This extra check helps avoid a common modeling mistake: removing a water simply because it is water, rather than deciding whether that particular molecule belongs in the model.
What if a molecule must stay?
Some arbitrary molecules and cofactors need topology files before they can be included in a GROMACS simulation. If you want to keep such a molecule, do not erase it during cleanup. Instead, obtain or generate its topology files (such as an .itp file) with an appropriate external tool, for example the ATB Server or CGenFF, and provide them during the GROMACS Wizard preparation step. The specific parameterization requirements depend on the molecule and workflow.
If you are unsure whether a small molecule is needed, pause before deleting it and check the purpose of the system. Cleanup decisions are easiest to reverse before you continue, so keeping an untouched copy of the original structure is also a sensible safeguard.
A practical order of operations
- Load the structure—for example, fetch PDB entry 1AKI.
- Identify the molecules and waters you intend to simulate.
- Remove alternate locations and only those small molecules, waters, or ions that are unnecessary for your model.
- Inspect the resulting structure before continuing.
- Proceed to GROMACS Wizard preparation, where you define the simulation model, box, solvent, ions, and project files.
The key is to make cleanup decisions based on the scientific model, not just on what can be removed. For the complete walkthrough and interface details, learn more in the GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.