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 →

BOMB is a separate program, not built on this one — it grows candidate molecules inside a binding site in its own right, and the analogs it proposes can then be taken up by MCPRO for free-energy refinement.

Run BOSS

Run a calculation.

Give us a molecule and pick a calculation. It runs on the Foundation's own parameter service — 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 and dihedral scans all run here. Monte Carlo simulations and free-energy perturbations do not: those take hours to days, so for those you download BOSS and run them yourself — and this page writes the command for you.

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: we build one for you, using LigParGen, which also assigns the OPLS force-field parameters.
  2. Choose what to find out. The short jobs run here. The long ones stay listed, but say so and hand you the command to run at home.
  3. Read the answer on this page — the energy, where it comes from, the structure in 3D, and the files behind it.

If you would rather run it yourself, everything here has an equivalent command; see download and install.

1 Your molecule

Hydrogens are added automatically.

2 What to calculate
Advanced — where the parameters come from

BOSS does not read a SMILES string. It needs a Z-matrix carrying OPLS atom types and partial charges, and LigParGen is what produces one. That happens automatically — these settings only matter if you need to match an earlier calculation.

Before BOSS can run, the molecule needs OPLS parameters. Choose Original only to work with parameters generated before the rewrite: the two engines number atoms differently and their charges differ slightly, so a result from one is not interchangeable with the other. LigParGen explains the difference in full.

The partial charges every calculation below is built on. LBCC is the corrected model and is defined for neutral molecules only; for an ion use 1.14*CM1A.

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 puts the molecule in a box of solvent and lets it move. There is no separate FEP entry because BOSS has none: a free-energy perturbation is a Monte Carlo run driven by coupling values, and the two annihilation entries prepare the Z-matrix it needs.

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. The named solvents put the molecule in a box of individual solvent molecules — most realistic, and slowest. Only gas phase runs here; the others still build the command for your own copy of BOSS.

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.
The search strategy for finding the lowest-energy shape. They all reach the same place on well-behaved molecules; conjugate gradient is a sensible default. Simulated annealing is for awkward cases where the others get stuck.
How long to let it run. For a minimization this caps the refinement cycles — the default is plenty for a small molecule. For other jobs this same number means something different, and the label changes to tell you.

How much detail goes into the output file. The default prints the coordinates without the table of every interatomic distance, which is what you usually want.

Why the parameter file is not written for you. A complete .par is pargen's answers with oplsaa.par appended, and the manual explains what every variable means without ever showing the file's layout. Writing one here would mean guessing at a format, and a wrong parameter file fails silently rather than loudly — so the page gives you pargen's answers instead, and lets BOSS write the file.

How to cite

If BOSS did the work, cite it.