Category: User tips and tutorials

“GROMACS uses periodic boundary conditions, combined with the minimum image convention: only one – the nearest – image of each particle is considered for short-range non-bonded interaction terms. For long-range electrostatic interactions this is not always accurate enough, and GROMACS therefore also incorporates lattice sum methods such as Ewald Sum, PME and PPPM.” (GROMACS Manual: Periodic boundary conditions) GROMACS Wizard supports the following shapes for space-filling unit cells: Cubic, Orthorhombic, Triclinic, Rhombic dodecahedron, Truncated octahedron. You can choose which unit…

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This section is part of the GROMACS Wizard tutorial. Once the system has been preprocessed and validated we can start the preparation step. In order to launch GROMACS simulations, we first need to prepare the system: choose the model (force field, solvent, ions), and define the periodic box. During the preparation step, GROMACS Wizard will generate a model, and add solvent and ions if necessary. Choosing the results folder First, let’s choose a folder where we would like the results…

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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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In this tutorial, we will show how to export atoms positions (for all atoms in the system or for a selection of atoms) along paths in PDB files thanks to the Export Along Paths app. This could be useful for example if you want to generate reaction coordinates for free energy calculations.   Requirements Export Along Paths Extension Before starting the tutorial, please download the 1pv7_ligand_complex_with_paths (~13 MB) which contains files for this tutorial. Tutorial Launch SAMSON. Load 1pv7_ligand_complex_with_paths.sam file…

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The Nudged Elastic Band (NEB) method allows for finding saddle points and minimum energy paths between known conformations. The method optimizes a number of intermediate images along the path by finding the lowest possible energy for each image while maintaining equal spacing between neighboring images. This constrained optimization is done by adding spring forces. The NEB method can be used, for example, to determine transition paths between already obtained structures corresponding to local energy minima (obtained using, e.g., the FIRE…

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