Category: User tips and tutorials

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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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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In this post, we will show how to use the Ligand Path Finder app for finding possible ligand unbinding pathways from a protein. Content Requirements Tutorial Loading the input model Launching the Ligand 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 Requirements…

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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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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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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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In this tutorial, we will show you how to use the ARAP Interpolation Path Extension to generate a path between two protein structures or conformations within a few seconds thanks to ARAP (As-Rigid-As-Possible) interpolation. References: Minh Khoa Nguyen, Léonard Jaillet, and Stéphane Redon. As-Rigid-As-Possible molecular interpolation paths. Journal of Computer-Aided Molecular Design (2017) 31: 403. https://doi.org/10.1007/s10822-017-0012-y Requirements ARAP Interpolation Path Extension Before starting the tutorial, we would like to ask you to download this file (ArapInterpolation) which contains the necessary…

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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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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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