Pathlines: show a path of the center of mass of an atomic system

In this post, we will show you how to create pathlines thanks to the Pathlines visual model. Pathlines are visual models which represent the trajectory of the center of mass of selected atoms along selected Paths. Pathlines may be used to understand the motion of a single atom, or a group of atoms, along a path/trajectory. Before starting the tutorial, please, download this archive: Pathlines (~13MB). It contains a file (1pv7_ligand_complex_with_paths.sam) from the Ligand Path Finder tutorial with already computed…

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Interactive Modeling Universal Force Field (IM-UFF)

Introduction We previously proposed ([1]) a new implementation of the UFF interaction model introduced by Rappe et al. in [2], combined with an automatic scheme to perceive the molecular system in order to compute the bonds, bond orders, and atoms’ types. If interested, you can read our previous post about this interaction model. This post is about the Interactive Modeling Universal Force Field (IM-UFF) interaction model that was published in [3] and which extends the UFF force field for performing…

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Universal Force Field

Introduction This post presents the basics about the Universal Force Field (UFF) interaction model. This interaction model implements the UFF force fields proposed by Rappe et al. in [1]. It also includes an automatic scheme to perceive the molecular system in order to compute the bonds, bond orders, and atom types, so that UFF can directly be applied on a given molecular system. For more details regarding this UFF  implementation and the approach used to automatically perceive the molecular structure,…

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Generating a path between protein structures

In this tutorial, we will show you how to use the ARAP Interpolation Path Extension for generating a path between two protein structures or conformations. Let us start with a list of requirements, then a tutorial on how to use the app. Requirements ARAP Interpolation Path App Before starting the tutorial, we would like to ask you to download this file (ArapInterpolation) which contains necessary files for this tutorial. After extracting it, you will have two pdb files: 1ddt_A.pdb and…

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Ligand unbinding pathway search

Hi everyone, In this post, I will show you how to use the Ligand Unbinding Pathway Search app for finding possible ligand unbinding pathways from a protein. Let us start with a list of requirements, and then a tutorial on how to use the app. Requirements SAMSON 0.7.0 The Ligand Unbinding Pathway Search app The GROMACS force field interaction model The FIRE state updater Before starting the tutorial, I would like to ask you to download this file (LigandUnbindingPathSearch) which…

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Protein conformational transition search

Hi everyone, In this post, I will show you how to use the Protein Conformational Transition Search app for finding possible paths between two conformations of a protein. Let us start with a list of requirements, and then a tutorial on how to use the app. Requirements SAMSON 0.7.0 Protein Conformational Transition Search app GROMACS force field interaction model FIRE state updater Before starting the tutorial, I would like to ask you to download this file (ProteinPathSearch) which contains necessary…

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Using the SMILES Manager

In this tutorial, you will learn how to use the SMILES Manager extension of SAMSON. This extension is based on RDKit. As some of you know, RDKit is an open-source toolkit for cheminformatics which is widely used. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. We will present these two sections one by one as they are totally independent. In…

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Building carbon nanotube models with SAMSON

In this quick tutorial, we will show you how to easily generate carbon nanotube (CNT) models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Extension that you can find on the SAMSON Extensions web page. If you need help with installing new SAMSON Extensions to your SAMSON installation, please visit User guide: Adding Extensions from SAMSON Connect. If you need help with installing SAMSON itself, please visit User guide: Installing SAMSON. Note: you can check whether you have…

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Generating crystal models

The Crystal Creator SAMSON Extension contains the basic tools to write and manipulate crystals. I will show you here how to use it. Read a crystal structure To have your first crystal, you can import one. With the Crystal Creator App, you can load CIF (Crystallographic Information File) files. First, go fetch some nice crystals on those 2 websites : The American Mineralogist Crystal Structure Database : http://rruff.geo.arizona.edu/AMS/amcsd.php The RRUFF Project Database : http://rruff.info/ I personally advise you to test…

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Calculating non-linear normal modes

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension is an advanced version of the Normal Modes Analysis SAMSON Extension also available on SAMSON Connect. This SAMSON Extension computes 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…

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