What it is

A better rule book for simulating molecules.

To simulate how a protein or RNA molecule moves, a computer needs a set of rules for how its atoms pull together, push apart, bond, and — most importantly — twist around one another. That set of rules is a force field. OPLS-AA, built over decades in the Jorgensen group at Yale, is one of the most widely used.

OPLS-AA/M is its refined version for proteins and RNA. Using high-accuracy quantum-chemistry calculations as the reference, the group re-tuned the “twisting” (torsional) energetics — the part that most controls how a chain folds and flexes — so that simulated molecules behave far more like the real ones measured in the lab. Everything else about OPLS-AA is kept, so it stays compatible with the group’s other tools.

In short: more realistic simulations of proteins and RNA in water — the groundwork for understanding how biomolecules work, and for computer-aided drug design.

Build a topology

Your structure, in one step.

Upload a protein and get a ready-to-simulate GROMACS topology, built with OPLS-AA/M — no local setup.

How it works & your privacy

What happens: your file is sent securely to our server, which strips out waters and other heteroatoms, runs GROMACS pdb2gmx with the OPLS-AA/M force field, and returns a zip containing the topology (topol.top, per-chain .itp), position restraints, processed coordinates (conf.gro), and the run log. It takes a few seconds.

Your privacy: the structure is processed in a temporary folder that is deleted immediately afterwards — nothing is stored, logged, or shared, and no third parties are involved. Once your download finishes, no copy remains.

Good to know: it works on standard-residue proteins (up to ~50,000 atoms). If a structure can’t be processed — a non-standard residue or missing atoms — you’ll see the exact GROMACS message so you know what to fix. Prefer to run it yourself? The force-field files are below.

Download

Parameters & topologies.

Ready-to-use files for GROMACS and CHARMM. Use requires geometric Lennard-Jones combining rules and 1,4 intramolecular nonbonded scaling.

Proteins

Protein parameters.inp Protein topology.inp GROMACS bundle.zip

RNA

RNA parameters.inp RNA topology.inp

How to use

Run it in your engine.

GROMACS

Unzip the GROMACS bundle to get the oplsaam.ff force-field directory, drop it in your working directory (or $GMXLIB), then build a topology. TIP4P is the water model used in the OPLS-AA/M validation (TIP3P also works):

unzip GMX_OPLSAAM.zip        # → oplsaam.ff/
gmx pdb2gmx -f protein.pdb \
    -ff oplsaam -water tip4p -ignh

CHARMM

Read the OPLS-AA/M topology and parameter files into your CHARMM script before building the structure:

read rtf   card name top_opls_aam.inp
read param card name par_opls_aam.inp

Requirements: geometric Lennard-Jones combining rules and 1,4 intramolecular nonbonded scaling. Match your engine's settings to these before running.

Used worldwide

Adopted across the field.

—+

citations in the research literature since 2015

—countries publishing

—most active

Fewer More

Citation count from Google Scholar, October 2026. Map from the peer-reviewed research citing OPLS-AA/M (Robertson et al., J. Chem. Theory Comput. 2015; via OpenAlex). Map: simple-world-map, CC BY-SA 3.0.

How to cite

References.

Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field. J. Chem. Theory Comput. 2015, 11, 3499–3509. doi:10.1021/acs.jctc.5b00356

Robertson, M. J.; Qian, Y.; Robinson, M. C.; Tirado-Rives, J.; Jorgensen, W. L. Development and Testing of the OPLS-AA/M Force Field for RNA. J. Chem. Theory Comput. 2019, 15 (4), 2734–2742. doi:10.1021/acs.jctc.9b00054