Program

BOSS

Biochemical and Organic Simulation System — the Monte Carlo engine this group's work is built on, and the program the rest of the software here calls.

Run BOSS Download BOSS
What it is

One engine, four decades of use.

BOSS is a general-purpose molecular modelling system that performs molecular mechanics calculations, Metropolis Monte Carlo statistical-mechanics simulations, and semiempirical AM1, PM3 and PDDG/PM3 quantum-mechanics calculations.

Free-energy perturbation in Monte Carlo simulation started here — the group introduced the method in 1985 — and BOSS is where it runs for organic molecules and solutions: free energies of solvation, conformational equilibria, reactions in solvent. The protein–ligand binding free energies behind our lead-optimization campaigns are computed in MCPRO, which is derived from this code.

What runs on it

Most of what we build sits on top of this.

BOSS is not one tool among several — it is the layer these stand on. One is derived from it; the other calls it every time somebody uses it.

  1. MCPRO

    Derived from BOSS. The same Monte Carlo machinery, reorganised around the concept of residues so it can handle peptides, proteins and nucleic acids in solution — and compute protein–ligand binding free energies by FEP.

    MCPRO →

  2. LigParGen

    Calls BOSS. Paste a molecule into the web server and BOSS runs on our machines to work out its OPLS-AA atom types and 1.14*CM1A partial charges; the server writes the result out in a dozen packages' formats. Every one of its citations is somebody running this engine.

    LigParGen →
Run BOSS

Run a calculation.

Give us a molecule and pick a calculation. It runs on the lab's own servers — nothing for you to install, and the answer comes back on this page in a few seconds. Energy minimizations, single-point energies, conformational searches, normal-mode frequencies, dihedral scans, atomic charges and GB/SA free energies of hydration all run here, in the gas phase or in GB/SA water, with the procedures BOSS itself ships (its x scripts), and you can download the folder to run it again on your own computer. Monte Carlo simulations and free-energy perturbations take hours to days, so this page prepares them for you: a folder with BOSS's own command and parameter files filled in for your molecule, and BOSS's README for the procedure, ready to run with BOSS on your own computer.

Never used BOSS? Read this first

BOSS is a molecular simulation program. You give it a molecule and a question — what shape does this take, how much energy does it have, what conformers exist — and it does the physics.

  1. Give it a molecule. Draw it, paste a SMILES string, type a name, or upload a file. You do not need a Z-matrix: BOSS's own converter (xMOLZ, or xPDBZ, xMOL2Z or xGJFZ for a file) builds one, with OPLS-AA atom types and 1.14*CM1A charges, exactly as on your own copy of BOSS.
  2. Choose what to find out. The short jobs run here. The long ones give you a folder of BOSS's own files, ready to run with BOSS on your own computer.
  3. Read the answer on this page — the energy, where it comes from, the structure in 3D, and the files behind it.

Every result comes with the folder BOSS ran in and BOSS's own README for its scripts, so you can run it again on your own copy; see download and install.

1 Your molecule

Hydrogens are added automatically.

2 What to calculate
Energy-minimize finds the molecule's most comfortable shape. Single-point measures the energy of the shape you already have. A conformational search hunts for the shapes it can adopt and ranks them. Normal modes gives vibrational frequencies and tells you whether a structure is a true minimum. A dihedral scan rotates one bond through a full turn and maps the energy. A Monte Carlo simulation lets the molecule move, alone, in GB/SA water or in a box of solvent. The FEP free energy of hydration switches the molecule off in the gas phase and in water. The last five take hours to days: you get them ready to run with BOSS on your own computer.

What surrounds the molecule. Gas phase is the molecule alone — fastest, and fine for comparing shapes. GB/SA treats solvent as a smooth continuum: much faster than real solvent and usually good enough. A box of individual solvent molecules is a Monte Carlo simulation: see the last calculations in the list.
How the energy is worked out. The OPLS force field treats atoms as balls and springs: fast, and it is what this group built. The semiempirical QM methods approximate the electrons instead — slower, but necessary if bonds are breaking or forming.
How to cite

If BOSS did the work, cite it.