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 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…

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GROMACS Wizard

In this tutorial, we will present you GROMACS Wizard Extension, a SAMSON extension for system preparation and simulation both 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 and run GROMACS simulations locally or in the Cloud, and get the results as simulation trajectories and plots. It is shipped with one of the latest versions of…

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Interactive Ramachandran Plot

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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Covalent and non-covalent protein-ligand docking with the Fitted Suite by Molecular Forecaster

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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Protein docking with Hex

In this tutorial, you will see how to perform protein docking with the Hex SAMSON Extension. The Hex SAMSON Extension wraps the protein docking program Hex developed by Dave Ritchie (Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins: Structure, Function, Bioinformatics) Content Requirements First steps Validation of the system Preparation of the system Setup of the system Hex parameters Setup of the search domain Running the docking and more Results Performing further analysis…

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Docking ligands and libraries of ligands with AutoDock Vina Extended

In this tutorial, you will see how to dock ligands or libraries of ligands into proteins with AutoDock Vina Extended SAMSON Extension and how to visualize and analyze the results. The AutoDock Vina Extended SAMSON Extension wraps the popular protein-ligand docking program AutoDock Vina (O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461) and extends its functionality by providing…

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What’s new in SAMSON 2020 R2

The new SAMSON 2020 R2 release brings further improvements throughout the core of SAMSON: Custom color palettes Cumulative updates since SAMSON 2020 R1, including quick minimization, a new displacer editor, etc. Support for a new type of nodes, meshes, i.e. textured triangular surfaces. A variety of new features and fixes of reported issues. For developers: new functionality in the SAMSON API and a new module that allows you to view the functionality exposed by SAMSON Elements, which you can use in…

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Export atom trajectories along paths

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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Optimize transition paths with the Parallel Nudged Elastic Band (P-NEB) method

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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Protein Path Finder

In this post, we will show how to use the Protein Path Finder app for finding possible paths between two conformations of a protein. Content Requirements Tutorial Loading the input model Launching the Protein Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths…

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