A molecular structure can look ready for simulation while still containing details that complicate preparation: alternate atom locations, waters you do not intend to model, small molecules without available parameters, or ions that should be handled later. Removing everything that looks unnecessary is not always the answer, though. A ligand or active-site water may be essential to the question you are studying.
The useful goal of pre-processing is not simply to make a structure smaller. It is to decide, molecule by molecule, what belongs in the simulation—and to leave a clean starting structure for the main GROMACS preparation workflow.
Start with a deliberate cleanup
In SAMSON, load your structure using Home > Fetch and a PDB identifier, or open a structure file already on your computer. The GROMACS Wizard tutorial uses the 1AKI structure as an example. The fetch dialog is one way to begin:
Before running cleanup, ask what you want to simulate. If a ligand or cofactor is part of the system you are studying, do not remove it just because it is a small molecule. Keeping an arbitrary molecule may require providing a topology file, such as an .itp, during the later preparation step. The documentation points to tools such as ATB Server or CGenFF for generating parameters; the key practical point is to account for parametrization before deciding to keep a molecule.
What to remove—and what to check
Open Home > Prepare to pre-process the system. Common cleanup choices include removing alternate locations, unwanted ligands or other small molecules, water, and monatomic ions. Adding hydrogens at this stage is optional because GROMACS can also add them later.
These options are decisions, not a universal recipe. In particular, “remove water” may be inappropriate when the structure contains tightly bound or functional waters, such as waters in an active site. Consider whether each molecule is relevant to your model before deleting it. When in doubt, inspect the selection rather than assuming every water or small molecule is expendable.
Keep important waters; remove the rest selectively
If you want to preserve active-site waters while removing waters farther away, select structures, residues, or atoms in the active site first. Then right-click the selection in the Document view or Viewport and choose Expand selection > Advanced. Set the node type to Water and select waters beyond a distance from the active-site selection. The example image shows a 5 Å setting, but the appropriate distance depends on the system and the purpose of your model.
If available, use auto-update to preview the selection. Check that the highlighted waters are the ones you intend to remove, then confirm. Finally, right-click the selected waters and choose Erase selection. Previewing and verifying the selection is a small step that can help avoid deleting waters you meant to preserve.
A quick pre-flight check
- Have alternate locations been handled?
- Are the ligands and cofactors you want to study still present?
- Have you considered whether any waters are functionally important?
- Are unwanted monatomic ions removed?
- If you kept an arbitrary molecule, do you have or plan to provide its topology?
After cleanup, you should have a starting structure containing the molecules you intend to simulate. This is a pre-processing step—not a substitute for the subsequent preparation workflow, where you define the simulation model, box, solvent, ions, and project files.
For the complete walkthrough, including the selective water-removal steps, read the GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.