Loading and Preparing Protein Conformations for Pathway Exploration in SAMSON

If you’re studying protein dynamics, a common challenge is identifying conformational pathways between two known states. Before diving into complex simulations or heavy computations, one crucial step must be done right: loading and preparing your protein’s conformational models correctly. In the SAMSON integrative molecular design platform, this process is smoother than you might expect — as long as you follow a few key steps.

This guide explains how to load and prepare a pair of protein conformations (for example, the open and closed states of a protein like Adenylate Kinase) using SAMSON’s Protein Path Finder tutorial setup. If you ever ran into errors due to misaligned models, missing atoms, or non-matching residues, this walkthrough is for you.

Download the Sample System

To begin, navigate to Home > Download within SAMSON and paste the following URL as the source for your document:

This will load a pre-prepared document featuring chain A of Adenylate Kinase in two different conformations: the start (PDB ID: 4AKE) and goal (PDB ID: 1AKE) structures. These serve as the endpoints of your transition path search.

In the Document view, you’ll be able to inspect the two conformations as different models under the same document tree. This ensures that your atoms, residues, and chains are properly aligned structurally for meaningful path computation.

Tips for Working With Your Own Systems

While the sample file is already ready to go, here’s how to prepare your own protein conformations:

• Use SAMSON’s Home > Prepare tools to remove alternate locations, ligands, ions, and to add hydrogens.
• To fix missing residues or atoms, including hydrogen placement at specific pH levels, use the PDBFixer extension.

If your two conformations are in separate files, they must be concatenated into a single PDB file using the MODEL…ENDMDL format:

This ensures that SAMSON recognizes them as two conformational states within the same structure — a requirement for the Protein Path Finder app to function correctly.

Troubleshooting Alignment Issues

A common mistake is to try to compute conformational morphing between structures that are not properly aligned. Make sure that residue numbering, atom names, and overall topology match between both models. If you can’t align them visually or programmatically, even advanced path-finding algorithms won’t produce meaningful results.

Next Steps

Once conformations are loaded and verified, you’ll be ready to define active motion atoms, set up energy evaluations, and run the ART-RRT planner inside the Protein Path Finder app. Taking the time to ensure your models are compatible will save hours of troubleshooting later on.

To explore the full workflow and continue toward calculating realistic transition pathways, visit the detailed documentation page: Protein Path Finder tutorial on samson-connect.net.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.