GROMACS Wizard - Pre-processing of the system

This section is a part of the GROMACS Wizard tutorial.

Load the system

In this tutorial, we will be using 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 to their default values.

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

Pre-process the system

Before applying the Preparation step in GROMACS Wizard, we first need to pre-process the system, i.e. remove alternate locations, existing water, ligands, ions. You can easily do it using Home > Prepare:

• Remove alternate locations.

• Remove unnecessary small molecules (check the Remove ligands option). Make sure to not 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 if you do not need them in the simulation then 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 arbitrary molecules that you do not need in the simulation.

• Remove water.

  Note

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

• Remove monatomic ions.

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

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, 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 some distance that is 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 would like to simulate, then you will need to provide topology files (itp files) for them. You can generate the topology files for arbitrary molecules using various servers, e.g. the ATB Server or CGenFF server. If you have them then you just need to provide them in GROMACS Wizard and it will do the rest for you.