A molecular structure can look ready for simulation and still contain details that complicate preparation: alternate locations, waters you do not need, unwanted small molecules, or monatomic ions. Removing everything indiscriminately is not a safe shortcut, though. A ligand may be central to the study, and a crystal water may have a functional role.
The goal of pre-processing is to make a deliberate decision about what belongs in the simulation before building the simulation model. This walkthrough uses the GROMACS Wizard in SAMSON and the 1AKI structure as an example. The same reasoning is useful whenever you are cleaning a protein system for a later GROMACS workflow.
Start with the structure you intend to simulate
Load 1AKI through Home > Fetch by entering 1AKI under PDB or PDB (mmCIF), then clicking the matching Load button. If you already have a local structure file, open it with Home > Open. At this point, pause to check what the document contains. A cleanup step is only useful if you know which molecules are part of your scientific question.
In particular, decide in advance whether any ligands, cofactors, ions, or waters must be retained. The right choice depends on the system you want to study; the presence of a molecule in a downloaded structure alone does not tell you whether to keep it.
Use cleanup options selectively
Open Home > Prepare and consider the available cleanup options:
- Remove alternate locations to clean up alternate-position entries in the structure.
- Remove ligands only when the small molecules are not part of the system you want to simulate. If a ligand or cofactor matters to the study, do not remove it as part of a routine cleanup.
- Remove water only when removing all existing water is appropriate. Crystal waters can include tightly bound or active-site waters, so blanket removal may discard molecules you want to preserve.
- Remove monatomic ions when they are not needed in the starting system.
- Add hydrogens is optional at this stage because GROMACS can add hydrogens later.
The useful habit is to treat each option as a decision, not a checkbox to apply automatically. Confirm the result before moving on: the cleaned structure should contain the molecules you intend to include, not simply fewer molecules.
Keep important waters, remove others
If you want to remove waters outside an active site while retaining nearby waters, select structures, residues, or atoms that define the active site—for example, the ligand and nearby water. Right-click the selection in the Document view or Viewport, then choose Expand selection > Advanced.
In the dialog, set the node type to Water and choose waters beyond a distance from the selected active-site region. The auto-update option can preview the selection as you adjust it. Check which waters are selected before clicking OK; then verify the selection once more before choosing Erase selection. This preview-and-check step helps avoid deleting waters you meant to keep.
What if a molecule must stay?
Some arbitrary molecules may need topology files (.itp) before they can be included in a GROMACS simulation. The tutorial notes that such files can be generated with external tools such as the ATB Server or CGenFF, then supplied during the GROMACS Wizard’s preparation step. If you do not need a molecule and cannot provide the required topology, remove it deliberately; if you do need it, plan for its parametrization rather than deleting it by default.
Once cleanup is complete, continue to the preparation workflow to define the simulation model, box, solvent, ions, and project files. For the full procedure and related guidance, read the original GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.