A structure can look ready for simulation and still contain molecules that complicate preparation: alternate locations, unwanted ligands, waters, or monatomic ions. But “cleaning” is not always a matter of deleting everything that is not protein. Some waters may be functionally important, especially near an active site. A careful cleanup helps avoid both unnecessary topology problems and the loss of parts of the system you meant to study.
This workflow uses the 1AKI structure as an example and focuses on a practical question: when should you remove waters, and how can you remove only the ones outside a region you want to preserve?
Start by deciding what belongs in the model
Before editing the structure, make a short inventory of what you intend to simulate. Keep any ligand or cofactor that is part of your research question; removing it during cleanup would change the system you are preparing. Conversely, arbitrary molecules that you do not need may be removed if GROMACS cannot generate a topology for them. Molecules you do want to keep will need suitable topology files, such as .itp files, which can be generated with external tools such as the ATB Server or CGenFF and provided during the later preparation step.
In SAMSON, load a structure through Home > Fetch by entering 1AKI in the PDB or PDB (mmCIF) field, then use the matching Load button. A locally saved structure can instead be opened through Home > Open.
Use broad cleanup only when it fits your system
Open Home > Prepare and consider the cleanup options: remove alternate locations, remove ligands, remove water, and remove monatomic ions. Adding hydrogens here is optional because GROMACS can also add them later.
The key is to treat these as modeling decisions, not automatic housekeeping. In particular, removing all water is not appropriate for every system. If you want to retain tightly bound or active-site waters, do not use broad water removal without first considering which waters matter to your model. Likewise, check the ligand-removal choice against your intended system before applying it.
Remove waters outside the active site selectively
If you want to keep waters near an active site while removing more distant waters, use selection to define the region to preserve:
- Select a structure, residue, or atom in the active site—for example, a ligand or a water molecule.
- Right-click the selection in the Document view or Viewport, then choose Expand selection > Advanced.
- Set the node type to Water and choose beyond a distance from the selection. The example below shows water beyond 5 Å. Use auto-update to preview the selection, then click OK.
- Inspect the selected waters before deleting them. If the selection is correct, right-click it and choose Erase selection.
The preview-and-verify step matters: the distance selection is a way to identify candidate waters, not a substitute for deciding which molecules your model should contain. Check that the active-site reference selection is appropriate and that the waters selected for deletion are the ones you intend to remove.
Finish with a deliberate check
After cleanup, review the structure and confirm that the molecules you need remain. If the system includes cofactors or other arbitrary molecules, make sure they are either intentionally removed or have topology files ready for the subsequent preparation workflow. The cleaned structure can then move on to the GROMACS Wizard Preparation step, where you define the simulation model, box, solvent, ions, and project files.
For the complete workflow and additional details, see the GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.