Avoid Pathway Artifacts: How to Properly Set Up Your Protein System in SAMSON

One of the most common sources of error when exploring conformational transitions in proteins is an incorrectly prepared system. Structural inconsistencies, missing atoms, or mismatched residue numbering can not only cause software crashes but generate misleading results when modeling pathways.

In this blog post, we’ll walk through how to properly prepare and set up your protein system for transition path modeling using SAMSON and the Protein Path Finder app. Although SAMSON provides a clean pre-setup example, you’ll very likely want to work with your own models. Here’s how to avoid trouble from the start. 🧬

Why Proper System Preparation Matters

Many molecular modelers deal with multi-conformational files or structures extracted from simulation snapshots. While visually similar, such conformations might have different atom orders, missing residues, or different levels of completeness—leading to unrealistic transitions or app failures.

To ensure smooth pathfinding, your conformations must be aligned not only structurally, but also logically. This means same chains, residue indices, atom names, and overall atom order—across the conformations.

Step-by-Step: Preparing Your Own Model

Here’s a checklist to follow if you want to explore transitions between two protein conformations not included in the tutorial sample:

Remove alternate locations: Clean up alternative positions for atoms which may cause ambiguity.
Remove ligands, ions, and solvent: Simplify the system by isolating the protein unless those elements are critical.
Add hydrogens: Especially important if your next steps include energy evaluation or minimization.

Fix Missing Atoms or Residues

Some models—especially experimental ones—may be incomplete. If your structure lacks heavy atoms (e.g., entire side chains) or residues, you can use the PDBFixer extension to complete it. This tool also allows protonation state specification at desired pH values.

More information is available in the Protein Preparation & Validation tutorial.

Matching Two Conformations

If your start and goal conformations are in separate PDB files, you’ll need to merge them into a single multi-model file. Each conformation should be included between:

MODEL        1
... (start conformation)
ENDMDL
MODEL        2
... (goal conformation)
ENDMDL
END

MODEL 1

... (start conformation)

ENDMDL

MODEL 2

... (goal conformation)

ENDMDL

END

This format ensures SAMSON can load both as distinct models for analysis in the Protein Path Finder app.

Using Pre-Configured Setup

If you’re just getting started or want to test functionality first, you can load the sample Adenylate Kinase document provided in the tutorial. It already includes the start and goal conformations as well as prepared atom groups for analysis.

Following proper preparation ensures not only that the Protein Path Finder can run, but also that the transitions it models represent physically realistic protein motions.

To learn more, visit the complete documentation page here: Protein Path Finder Documentation.

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