Molecular docking with AutoDock Vina

In this tutorial, we will show how to perform molecular docking thanks to the AutoDock Vina SAMSON Element that 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). If you’d like to dock entire libraries of ligands instead of just one ligand, check out the SAMSON Element called AutoDock Vina Extended.…

More…

Export atoms 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 SAMSON version 0.7.0 or higher Export Along Paths Element Before starting the tutorial, please download the 1pv7_ligand_complex_with_paths (~13 MB) which contains files for this tutorial. Tutorial…

More…

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…

More…

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…

More…

Ligand Path Finder

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…

More…

Pathlines

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. Before starting the tutorial, please, download this archive: Pathlines (~13MB). It contains a file (1pv7_ligand_complex_with_paths.sam) from the Ligand unbinding pathway search tutorial with already…

More…

Building a SAMSON Element on Linux

Please, refer to the updated version: Developer guide: Building a SAMSON Element on Linux. This tutorial shows how to build SAMSON Elements on Linux using QtCreator. For other IDE, please, check the Main steps to configure a project for your SAMSON Element. This tutorial was done with QtCreator v.4.4.1 and Qt 5.9.3. For an older version, please, check SAMSON School 2017: Introduction and installation of the SAMSON SDK. If you experience any problems with building your SAMSON Element, please let…

More…

Building a SAMSON Element on Mac OS

Please, refer to the updated version: Developer guide: Building a SAMSON Element on Mac OS. This tutorial shows how to build SAMSON Elements on Mac OS using XCode. If you want to use QtCreator as the main IDE for developing SAMSON Elements you can follow the same steps and check the tutorial Building SAMSON Element on Linux. The tutorial applies for SAMSON version 0.7.0 and higher. For an older version, please, check SAMSON School 2017: Introduction and installation of the…

More…

Building a SAMSON Element on Windows

Please, refer to the updated version: Developer guide: Building a SAMSON Element on Windows. This tutorial shows how to build SAMSON Elements on Windows using Microsoft Visual Studio (MS VS). The tutorial applies for SAMSON version 0.7.0 and higher. For an older version, please, check SAMSON School 2017: Introduction and installation of the SAMSON SDK. If you experience any problems with building your SAMSON Element, please let us know on SAMSON-Connect forum. Content Requirements Configuration of a project in QtCreator…

More…

Generating a SAMSON Element

You can also access this tutorial in the Developer guide: Generating a SAMSON Element. This tutorial applies for SAMSON version 0.7.0 and higher. For an older version, please, check SAMSON School 2017: Introduction and installation of the SAMSON SDK. You can also check the documentation on the SAMSON Element Generator. Content The SAMSON SDK Element Generator Running the SDK Element Generator Reviewing the generated code The SAMSON SDK Element Generator The SDK Element Generator is a very useful tool, provided…

More…