Category: User tips and tutorials

This section is part of the GROMACS Wizard tutorial. Once the system has been preprocessed and validated, we can start the preparation step. To launch GROMACS simulations, we first need to prepare the system: Choose the model (force field and solvent). Choose the molecular system and, optionally, choose a set of conformations or a path for a batch project. Define the periodic box. Choose what and how many ions should be added. Run preparation During the preparation step, GROMACS Wizard…

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This section is part of the GROMACS Wizard tutorial. Once a system or a batch project has been successfully prepared, it is necessary to perform the Energy Minimization (EM) step to ensure that the system has no steric clashes or inappropriate geometry. Switch to the Minimize tab. Selecting input structure When launching the Energy Minimization step, GROMACS Wizard requires you to provide one of the following: The path to a GRO file resulting from the previous step: either a GRO…

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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 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 will appear asking about import parameters – you can leave them to their default values. If you…

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This tutorial presents the GROMACS Wizard Extension, a SAMSON extension for system preparation and simulation locally and in the Cloud using the well-known GROMACS package. The GROMACS Wizard Extension integrates the main GROMACS features into SAMSON – it provides the possibilities to easily prepare systems for simulation with GROMACS, run GROMACS simulations locally or in the Cloud, and get the results as simulation trajectories and plots. It ships GROMACS (the latest version of the extension ships GROMACS 2021.3) meaning that…

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In this tutorial, we will show you how to use the Interactive Ramachandran Plot SAMSON extension. First, go to SAMSON Extensions web page, log in, and add the Interactive Ramachandran Plot SAMSON extension. The Ramachandran plot is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. For this tutorial, you can open any protein you like. We will be using 1YRF. You can use the Protein Data Bank Downloader to fetch molecules from…

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In this tutorial, you will learn how to perform covalent and non-covalent protein-ligand docking with the FITTED Suite SAMSON Extension. The FITTED Suite SAMSON Extension was done in partnership with Molecular Forecaster and wraps their Fitted Docking software. FITTED stands for Flexibility Induced Through Targeted Evolutionary Description. This fully automated docking software is unique in that it considers the flexibility of macromolecules, the presence of bridging “displaceable” water molecules, covalent functional groups, and proton shifts upon metal coordination. FITTED is…

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In this tutorial, you will learn how to run a simple but powerful technique, called positional analogue scanning, in order to generate new analogs of your molecules directly in SAMSON using the SMILES Manager extension. This new functionality was inspired by this blog post from Pat Walters and this paper from Lewis Pennington, Ingo Muegge, and coworkers. It will allow you to evaluate the effects of newly introduced changes of your molecules on their properties, like the binding affinity (using Autodock Vina Extended SAMSON…

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In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module and indicate the desired number of modes,…

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