Stop Wasting Time on Broken Protein Structures: A Simple Guide to Preparing Protein Models in SAMSON

If you’re working with experimental protein data, chances are your structure files come with imperfections: alternate locations, missing atoms, ligands you don’t need, or solvent cluttering your simulation. For molecular modelers, preparing the system properly is not just optional—it’s the only way to get meaningful results from simulations like energy minimizations or transition path searches.

In this blog post, we’ll guide you through preparing protein systems in SAMSON, focusing specifically on pre-processing structures for use with the Protein Path Finder app. This procedure can help streamline your workflow and ensure reliable results.

Why is protein preparation important?

Even high-resolution experimental structures often include artifacts—missing hydrogens, alternate locations, or crystallization agents. These can interfere with simulations and bias your energy evaluations. Before launching any kind of structural calculation, from minimizations to conformational pathway searches, a proper cleanup is necessary.

What the Protein Path Finder expects

The Protein Path Finder uses the ART-RRT algorithm to search transition pathways between two protein conformations. To work properly, the input system must:

Be prepared: only contain the protein, no ligands, ions, or solvent.
Have consistent atom naming, residue ordering, and atom counts across conformations.
Contain added hydrogens.
Use a single .pdb file or SAMSON document with multiple models.

How to prepare your system

In SAMSON, go to Home > Prepare and apply the following actions:

Remove alternate locations to eliminate ambiguous atomic positions.
Remove ligands, solvent, and ions unless you specifically need them.
Add hydrogens to ensure proper valency and interaction modeling.

Fixing incomplete structures

If your protein is missing side-chain atoms or entire residues, download the PDBFixer extension. This handy plugin lets you:

Repair missing heavy atoms and residues.
Add hydrogens based on pH conditions.

This ensures structural consistency before combining conformations in one document.

Merging multiple conformations

If you have two conformations in separate files, make sure both are consistent (same chain IDs, residue numbers, and atom names). You can combine them manually into a single .pdb file using the following format:

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

MODEL 1

... (start conformation)

ENDMDL

MODEL 2

... (goal conformation)

ENDMDL

END

SAMSON can also handle this through the document structure using models. Once merged, you can move on to energy minimizations or pathfinding tasks.

Where to go from here

Mastering protein preparation ensures that your downstream analysis—like pathway prediction, binding analyses, or minimizations—runs smoothly and produces results you can trust. Whether you’re modeling conformational changes or running exploratory simulations, a clean starting structure makes all the difference.

To learn more about the preparation, download samples, and begin path predictions, visit the Protein Path Finder tutorial.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from the official site.