GROMACS Wizard – Pre-processing of the system

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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 or you can easily get it using the Protein Data Bank Downloader Extension (you can add this free extension from the SAMSON Connect). Open this extension via Apps menu > Biology > Download from Protein Data Bank or simply search for it in the Find commands search box in the top-right corner of SAMSON, 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 will appear asking about import parameters – you can leave them to their default values.

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

Validation of the system

Before applying the Preparation step in GROMACS Wizard, we first need to validate and preprocess the system.

Removing alternate locations

If the system contains atoms with alternate locations, then they need to be removed. The 1AKI system used in this tutorial does not have any alternate locations so you do not need to apply this step.

To check for alternate locations and to remove them, go to Biology menu > Prepare > Structure validation – this should open an extension. Please note, that to use the Structure validation functionality you need to have at least the Standard plan – you can subscribe to the trial period on SAMSON Connect – Plans. In this tutorial example, the system has no alternate locations and therefore there is no need to use the Structure validation module, so if you don’t have access to it you can simply skip to the next section.

In the Alt. locations tab, click on the Find alternate locations button. If there are any, they will be shown in the table. In this tutorial example, there are no alternate locations, but if there were any it would be necessary to remove them by clicking on the Remove alt. locations button. You can also select which alternate locations to delete in the table.

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.

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.

To delete all the existing water molecules from the system, go to Biology menu > Select > Water – this should select all water molecules from the current selection or from the document if nothing is selected.

Then right-click on the selection in the Document view or in the Viewport and click Erase selection.

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 in 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 in the Viewport and click Erase selection.

Removing arbitrary molecules

The 1AKI system used in this tutorial does not have any arbitrary molecules so you do not need to apply this step.

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 go to Biology menu > Select > Ligands – this should select all small molecules from the current selection or from the document if nothing is selected – verify the selection and erase arbitrary molecules that you do not need in the simulation.

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.

 

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