A structure can look ready for simulation and still contain details that complicate preparation: alternate locations, extra small molecules, ions, or waters that are not needed. But “cleaning” does not always mean deleting everything that is not part of the protein. Some waters and ligands may be important to the system you intend to study. A careful first pass can prevent avoidable preparation problems while helping you preserve what matters.
This workflow uses the GROMACS Wizard in SAMSON and the example structure 1AKI. The main idea is to make each deletion deliberate: decide what belongs in the simulation, remove only what you do not need, and check selections before erasing them.
Start with the model you actually want to simulate
Load 1AKI from Home > Fetch by entering 1AKI under PDB or PDB (mmCIF), then choosing the corresponding Load button. You can also open a structure file already on your computer. The important step is not the source of the file; it is deciding which components should be part of your simulation before moving on to preparation.
A practical cleanup checklist
Open Home > Prepare and consider these options:
- Remove alternate locations. Alternate locations can represent multiple positions for atoms in a structure. Removing them helps avoid carrying those alternatives into the next stage.
- Remove ligands only if they are not part of the system you want to simulate. If a ligand or cofactor is scientifically important, keep it rather than treating every small molecule as disposable.
- Remove water only when removing all water is appropriate for your model. This may be unsuitable when tightly bound or active-site waters have a functional role.
- Remove monatomic ions when those ions are not needed in the starting structure. Ions can be handled later as part of the preparation workflow.
- Add hydrogens is optional at this stage, since GROMACS can also add them.
Keep useful waters; remove distant ones selectively
One common source of uncertainty is crystal water. Removing every water molecule is convenient, but it can also remove waters that are tightly bound or function in an active site. If you want to preserve those waters while clearing others, select something that defines the region to keep—for example, a ligand, a water, a residue, or atoms in the active site.
Right-click the selection in the Document view or Viewport, then choose Expand selection > Advanced. Set the node type to Water and select waters beyond a chosen distance from the active-site selection. The documentation illustrates this with a 5 Å distance; treat that as an example, not a universal cutoff. The appropriate distance depends on the system and the waters you intend to retain.
If available, turn on auto-update to preview the selection. Before deleting anything, inspect which waters are selected. Then right-click the verified selection and choose Erase selection. This preview-and-check step is especially useful when a broad selection could remove molecules you meant to keep.
Do not leave wanted molecules unprepared
If you keep an arbitrary molecule in the simulation, it may need a topology file, such as an .itp file. The tutorial mentions external tools such as the ATB Server or CGenFF for generating topology files, which can then be provided during the GROMACS preparation step. If a molecule is not needed and cannot be parameterized for your workflow, removing it may be the simpler choice—but make that decision based on the model you intend to study.
After cleanup, you should have a starting structure containing the components you mean to simulate, ready for the next GROMACS Wizard preparation step. For the complete walkthrough and related guidance, see the GROMACS Wizard pre-processing documentation.
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