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A high-performance QM/MM program


QSite is a multi-scale simulation tool that utilizes the QM/MM method, which combines the principles of quantum mechanics and molecular mechanics. It is designed to accurately predict the molecular configurations, energetics, and the electronic structures of a reactive system through quantum chemical treatment of atoms, providing crucial insights into reactive chemistry essential for understanding chemical transformation in the presence of intermolecular interactions. QSite is equally applicable for describing non-reacting chemical systems.

Key Capabilities

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High performance

Outperforms other QM/MM programs because it takes advantage of Jaguar, long recognized as the industry leader in QM calculations.

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Advanced technology

Provides an innovative approach to the QM/MM interface specifically addressing protein systems and interactions between QM and MM regions.

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Transition metal convergence

Achieves a high degree of accuracy in metalloproteins thanks to Jaguar’s advanced capabilities; it reliably and efficiently converges to the correct ground state of transition metal containing systems.

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Wavefunction choices

Offers different levels of theory to evaluate the QM region: Hartree Fock, DFT, and local MP2. This allows the user to choose the best balance between computational cost and accuracy.

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Advanced calculation setup and analysis

Automatically applies special interface parameters, making it simple to set up calculations. Computed results, such as molecular orbitals and electron densities, can be visualized within Maestro.

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Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

Materials Science
Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores
Life Science
Light Harvesting by Equally Contributing Mechanisms in a Photosynthetic Antenna Protein
Life Science
Dioxygen Activation in Methane Monooxygenase: A Theoretical Study
Life Science
Mixed ab initio QM/MM Modeling Using Frozen Orbitals and Tests with Alanine Dipeptide and Tetrapeptide
Life Science
A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-scale Modeling of Chemistry in Protein Environments
Life Science
Hydroxylation of Methane by Non-Heme Diiron Enzymes: Molecular Orbital Analysis of the C-H Bond Activation by Reactive Intermediate Q
Life Science
Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase
Life Science
Reversible Dioxygen Binding to Hemerythrin
Life Science
How Iron-containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations
Life Science
Peripheral Heme Substituents Control the Hydrogen-Atom Abstraction Chemistry in Cytochromes P450

Training & Resources

Online certification courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.


Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.