SAMSON Extensions Tutorials

Use these tutorials to follow task-based workflows with SAMSON Extensions, from docking and molecular dynamics to materials science, DNA origami, modeling, and analysis.

Before you start

Most tutorials are hands-on. While you read, add the extension mentioned in the tutorial, open SAMSON, and load the sample system or input data when the page asks for it.

If you are new to SAMSON itself, start with the SAMSON User Guide before following advanced extension workflows.

Find a tutorial by task

I want to...	Start with	Extension / tool	Level	Expected result
Dock ligands or ligand libraries	Dock ligands and libraries of ligands with AutoDock Vina Extended	AutoDock Vina Extended	Beginner / intermediate	Docking poses and scores
Dock protein-ligand complexes with covalent or non-covalent options	Covalent and non-covalent protein-ligand docking with the Fitted Suite	FITTED Suite	Intermediate	Protein-ligand docking results
Dock two proteins	Protein docking with Hex	Hex	Intermediate	Ranked protein-protein docking poses
Run molecular dynamics	GROMACS Wizard tutorials	GROMACS Wizard	Intermediate	Prepared, minimized, equilibrated, and simulated system
Prepare a protein	Protein preparation and validation	Protein preparation tools	Beginner	Cleaned and validated protein structure
Analyze ligand strain	Strain Explorer	Strain Explorer	Beginner / intermediate	Local and global ligand strain estimates
Build a crystal	Generate crystal models	Crystal Creator	Beginner	Crystal structure in SAMSON
Build nanotubes	Build carbon nanotube models	Nanotube Creator	Beginner	Single-walled or multi-walled nanotube model
Design DNA origami	Design DNA nanostructures with Adenita	Adenita	Intermediate	DNA nanostructure model
Build molecular boxes	Create molecular boxes with Molecular Box Builder	Molecular Box Builder	Beginner / intermediate	Molecular box or lipid-layer system
Compute transition paths	Generate a transition path with ARAP Interpolation	ARAP Interpolation	Intermediate	Smooth path between protein conformations
Find ligand unbinding paths	Ligand Path Finder	Ligand Path Finder	Intermediate	Candidate ligand unbinding pathways

Recommended first tutorials

• Protein preparation and validation - start here before many protein modeling, docking, or simulation workflows.
• Dock ligands and libraries of ligands with AutoDock Vina Extended - follow a practical protein-ligand docking workflow.
• Generate crystal models - build and inspect crystal structures.
• Fast geometry optimization with FIRE minimizer - learn a reusable minimization tool used in several workflows.

Tutorial families

• GROMACS Wizard tutorials - prepare, minimize, equilibrate, simulate, and analyze molecular systems with GROMACS Wizard.
• Docking tutorials:
• AutoDock Vina Extended for ligand and ligand-library docking.
• FITTED Suite for covalent and non-covalent protein-ligand docking.
• Hex for protein-protein docking.
• SMILES Manager tutorials:
• Using the RDKit - SMILES Manager
• Perform Positional Analogue Scanning using the SMILES Manager
• Symmetry tutorials:
• Generate symmetry mates for proteins
• Symmetry detection in biological assemblies

Tutorials by domain

Drug discovery and structural biology

• Compute normal modes that open a binding site
• Explore the SARS-CoV-2 spike opening motion
• Create coarse-grained models for the MARTINI force field using Martinize2
• Dock ligands and libraries of ligands with AutoDock Vina Extended
• Covalent and non-covalent protein-ligand docking with the Fitted Suite
• Protein docking with Hex
• Prepare, minimize, equilibrate, and simulate using GROMACS Wizard
• Generate a transition path between protein structures with ARAP Interpolation
• Ligand Path Finder
• Protein Path Finder
• Molecular Restrainer: energy minimization for NMR-derived structures
• Predict protein-ligand complexes using NMR2
• Predict Biomolecular Structures
• Protein alignment
• Protein preparation and validation
• Interactive Ramachandran Plot
• Strain Explorer: analyze ligand strain and compare relaxed conformations
• Generate symmetry mates for proteins
• Symmetry detection in biological assemblies

Materials science

• Build carbon nanotube models
• Generate crystal models

DNA origami

• Design DNA nanostructures with Adenita

Molecular modeling, force fields, and utilities

• Build custom polymers with Polymer Builder
• Create molecular boxes with Molecular Box Builder
• Export atoms trajectories along paths
• Fast geometry optimization with FIRE minimizer
• Interactive Modeling Universal Force Field
• Making nano-batarangs and more with Simple Script
• Optimize transition paths with P-NEB
• Pathlines: visualize motion of the center of mass of an atomic system
• UMA Force Field
• Universal Force Field

Related resources

• Open the SAMSON User Guide for core SAMSON interface and workflow concepts.
• Use the Python Scripting Guide to automate SAMSON with Python.
• Ask questions in the Forum when you need help with a tutorial or extension.

Next step

If you want a complete molecular dynamics route, start with the GROMACS Wizard tutorials. If you are choosing among several scientific tasks, use the tutorial finder above.