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. You can download it from the RCSB Protein Data Bank website by clicking on Home > Fetch. Enter the PDB code 1AKI (you can select any format: PDB, PDBx/mmCIF, or MMTF), and click Load. 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:

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

If you want to have more control please check the section below.

Advanced: Validation of the system

Checking for alternate locations

If the system contains atoms with alternate locations, then they need to be removed.

Tip

You can remove alternate locations in a single step via Home > Prepare and checking the Remove alternate locations option.

You can check the system for alternate locations using Home > Validate - this will launch the Structure validation module. There in the Alt. locations tab, click Find alternate locations. If there are any, they will be shown in the table. If there are any, you can remove them by clicking on Remove alt. locations.

You can also perform other checks for your system if necessary, e.g. check bond lengths, non-standard residues, and clashes.

Removing existing water

Now we will delete the existing water molecules from the system.

Tip

You can remove water in a single step via Home > Prepare and checking the Remove water option.

Please note, that this procedure is not 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.

Tip

Alternatively, you can remove water as follows: click on Select > Water to select it in the document,

then in the pop-up context menu click on the Delete button (with the trash bin icon).

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.

Removing arbitrary molecules

Tip

You can remove non-protein molecules in a single step via Home > Prepare and checking the Remove ligands and Remove ions options.

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.

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.