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GROMACS Wizard - Protein-ligand systems#

From this tutorial you will learn how to prepare and simulate protein-ligand systems with GROMACS Wizard.

Note

This tutorial covers the case of non-covalently linked complexes. For covalently linked protein-ligand complex, some additional special treatment for parametrization of the linking bond is required.

Prerequisites#

Before proceeding with this tutorial, we recommend checking the following tutorials:

1. Ligand parametrization#

If your ligand is not a standard residue available in the force field you are going to use, you need to parametrize it for this force field.

You can parametrize your ligand using automated tools/servers, for example, the following ones depending on the chosen force field:

  • Antechamber - parametrizes molecules for AMBER.
  • ATB - a topology generation server for GROMOS96 54A7 force field.
  • CGenFF - a topology generation server for CHARMM force field.
  • LigParGen - a topology generation server for OPLS-AA force field.

Check which file formats are accepted as inputs by the tool/server that your are going to use.

Note

Please refer first to the Pre-processing of the system for GROMACS Wizard tutorial.

Add hydrogens#

Most of the parametrization tools/servers require a ligand to have all hydrogens properly set.

You can add hydrogens directly in SAMSON (Edit > Add hydrogens):

  • For standard ligands present in the Chemical Component Dictionary (CCD) it will add all hydrogens with their proper names as described in the CCD. If you downloaded the system from the Protein Data Bank, then, mostly likely, its ligands are present in the CCD.
  • For ligands that are not present in the CCD it will add hydrogens based on valences. So, your ligand should have aromatic rings and charges already specified. If you have a non-standard ligand in a file format that contains this info (e.g., .mol2), prefer to use this file for adding hydrogens in SAMSON.

You can also use any other external tools to add hydrogens, e.g. Open Babel.

Extract ligand from structure#

If your ligand is part of a protein-ligand complex, you will need to extract it from the complex to supply to a parametrization tool/server. For that, simply select the ligand in the Document view, and go to Home > File > Save selection as... and choose the file format acceptable by the parametrization tool/server you are going to use.

If you already have a ligand file with all the hydrogens added, then you can directly use it in the parametrization tool/server of your choice.

Tip

If the parametrization tool/server requires another file format, you can use SAMSON to covert between formats: load the file in SAMSON and save it into the required format.

Parametrization#

Now, use the parametrization tool/server of your choice to obtain the ligand's topology. In the end, you will need to obtain from the tool/server the following:

  • include topology file (.itp);
  • if available, an updated structure file for checking the structure;
  • optionally, the force field, if it uses some modified one (e.g., gromos54a7_atb from the ATB server).

Note

Some of these servers have a limit on the maximum ligand size. If your ligand has more atoms, then you can try to subdivide the ligand into chunks (sub-residues), possibly overlapping ones, and parametrize them separately with taking into account the connection between chunks. For this, please refer to the documentation and/or papers for the tool/server you are using.

2. Combine protein and ligand#

Now that you have your ligand parameterized, we strongly recommend you to download an updated structure file from the server, if available, to veryfy if the ligand structure had any modifications done by a parametrization tool/server, e.g., change in atom names.

If you already had you protein-ligand complex together and ligand structure hasn't changed (i.e., no atom name changes or new hydrogens added), then you can skip this step.

If you already have a ligand in the protein-ligand complex and want to replace it, then you can first position the new/updated ligand at the old ligand's position and then delete the old ligand.

If you don't have the ready-to-use protein-ligand complex then you will need to add your ligand to the system using one of the following ways:

  • Use any of the move objects functionalities available in SAMSON, e.g., use Move editors to manually place the ligand in the desired location.
  • Use AutoDock Vina Extended to dock the ligand into a binding pocket.
  • Append the ligand structure into the protein structure file - make sure the structures do not overlap in positions and are either placed in separate chains or have consecutive sequence numbering. If you need to convert file formats, you can load afile in SAMSON and save it in the required format.

Ensure that the ligand is named the same in the structure file and in the topology file (.itp) provided by a parametrization tool/server.

3. Prepare the protein-ligand system#

Open the GROMACS Wizard in SAMSON (Home > Apps > Biology > GROMACS Wizard) and switch to the Prepare tab.

Choose the protein-ligand system in the Document view in SAMSON and set it in GROMACS Wizard via Set system.

Prepare from Document

Tip

Please refer to the GROMACS Wizard - Step 1: Prepare tutorial for more information.

Provide ligand topology file#

Now, you need to provide the include topology file (.itp file) for the ligand, and GROMACS Wizard will do the rest for you. For that click on the Edit button for include topology files (itp) in the Choose model section:

Add .itp files

In the pop-up dialog, click on Browse and choose the necessary .itp file(s).

"Add .itp files" dialog

Please note that when you provide additional topology files then it might be necessary to provide the force field with which they were parametrized if it is not provided with the GROMACS Wizard by default. For example, if you generated ITP files using the ATB server then download the corresponding force field from this server (e.g., gromos54a7_atb from the ATB server). Please see the Provide custom force field section.

Provide custom force field#

If the parametrization server you used provides a custom force field (e.g., gromos54a7_atb from the ATB server), that is not available in GROMACS by default, the you will need to provide it in GROMACS Wizard. First download this custom force field from the server you used and then, in GROMACS Wizard, simply click on the Add button (Add) for force fields.

Add custom force field

You need to do it only once - the added force field will be stored by the GROMACS Wizard.

To remove an added force field from the list, click the Remove button (Remove). Please note, that it will remove all the added custom force fields, but the standard force fields will not be removed.

Prepare#

Please refer to the GROMACS Wizard - Step 1: Prepare tutorial for the other steps (choosing the solvent model, the periodic boundary box, ions, etc.), if you haven't already done them.

Once you finished with setting up the preparation parameters, click the Prepare button at the bottom of the tab to run the preparation step.

Note

Some pop-ups might appear informing you about the current steps or possible warnings/issues if there are any,. For example, a warning if using the gromos54a7 force field from the ATB server.

Tip

To view the log/output click on the Output button at the top of the GROMACS Wizard:

Open output

Once the preparation has been successfully done, the resulting system will be saved in the results folder, you will be asked whether you would like to load it in SAMSON (optional, if you want to check the prepared system), and you can proceed to the next steps.

Next steps#

For the next steps, please refer to the corresponding general tutorials: