GROMACS Wizard - Pre-processing of the system

In this tutorial, you will clean a molecular system before sending it to the main GROMACS preparation workflow. This step helps you remove data that often causes confusion later, such as alternate locations, waters you do not need, ligands you do not want to simulate, and monatomic ions.

Before you start

• Add GROMACS Wizard.
• For this walkthrough, use the 1AKI structure or a similar protein system.
• If your system contains ligands or cofactors that you do want to simulate, do not remove them during cleanup.

This section is part of the GROMACS Wizard tutorial.

Load the system

In this tutorial, we will use the 1AKI structure.

• Open Home > Fetch.
• Input 1AKI in PDB or PDB (mmCIF).
• Click the corresponding Load button. Depending on the format, a pop-up dialog might appear asking about import parameters; you can leave them at their default values.

If you downloaded the system from the Protein Data Bank website and have it locally on your PC, you can load your system using Home > Open (Ctrl/Cmd + O).

Pre-process the system

Before applying the Preparation step, clean the system with Home > Prepare:

• Remove alternate locations.

• Remove unnecessary small molecules (check the Remove ligands option). Make sure not to remove ligands that you want to simulate.

  Note

  If your system contains any cofactors or other arbitrary molecules for which GROMACS cannot generate topology, and you do not need them in the simulation, you can remove them either by selecting them in the Document view and erasing them or by going to Select > Biology > Ligands. This should select all small molecules from the current selection or the document if nothing is selected. Verify the selection and erase the molecules you do not need in the simulation.

• Remove water.

  Note

  Please note that this procedure might not be universally applicable. See the How to delete existing crystal waters outside of the active site section to delete only some water molecules and preserve water molecules that are functional in the system, e.g., tightly bound or active-site waters.

• Remove monatomic ions.

• The Add hydrogens option is optional since GROMACS can add hydrogens as well.

After this step, you should have a cleaner starting structure with only the molecules you want to keep for simulation.

See also

Please refer to the Protein Preparation & Validation tutorial for more information on how to prepare and fix protein systems.

How to delete existing crystal waters outside of the active site

Please note that if the system contains tightly bound or otherwise functional active-site water molecules, then the procedure described above might not be appropriate. To remove only water outside of the active site, follow the steps described below.

1. Select structures (e.g., ligand, water), residues, or atoms in the active site.
2. Right-click on the current selection in the Document view or the Viewport and in the context menu go to Expand selection > Advanced.

3. In the pop-up dialog, set Water as the Node type and choose beyond a distance outside of the active site. You can click on the auto-update option to see the selection. Click OK to select. Verify the selection.

   

4. Right-click on the selection in the Document view or the Viewport and click Erase selection.

Parametrization of arbitrary molecules

If your system contains arbitrary molecules that you want to keep in the simulation, you will need topology files (.itp) for them. You can generate those files with external tools such as the ATB Server or CGenFF. Once you have them, you can provide them later in the Preparation step.