BOSS Quick Start
Conformer search & GB/SA hydration
Free · on-site
A short BOSS job that gets a molecule ready for docking, quantum chemistry or MD. Submit a molecule — SMILES, drawn, by name, or a MOL/SDF/PDB file — and BOSS searches the shapes it can take in the gas phase, computes each one’s energy in water modelled as a continuum (GB/SA), and returns the most stable shape in water with its hydration free energy, dipole moment, surface area and volume, as SDF, MOL2, XYZ and PDB files. Every other shape it found can be viewed and downloaded too.
Jorgensen, W. L.; Tirado-Rives, J. Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297
Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field. J. Phys. Chem. B 2004, 108, 16264–16270. doi:10.1021/jp0484579
TIP3P, TIP4P & TIP5P
Interactive tool
Free · on-site
Put a molecule — SMILES, drawn, by name, or a MOL/SDF/PDB file — in TIP3P, TIP4P or TIP5P water and download it ready to run in GROMACS, OpenMM, LAMMPS, AMBER or BOSS: OPLS-AA parameters and charges from BOSS, and a water box built and simulated by BOSS with the water layer you choose, counter-ions and optional 0.15 M NaCl, with the density, radial distribution functions and hydrogen bonds from the BOSS run, and minimization, equilibration and 100 ns production scripts, in a few minutes.
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926–935. doi:10.1063/1.445869
Mahoney, M. W.; Jorgensen, W. L. A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions. J. Chem. Phys. 2000, 112, 8910–8922. doi:10.1063/1.481505
Organic Solvents
Solvent boxes
Free · on-site
Put a molecule — SMILES, drawn, by name, or a MOL/SDF/PDB file — in one of the organic solvents stored in BOSS (methanol, acetonitrile, chloroform, dichloromethane, carbon tetrachloride, DMSO, THF), and download it ready to run in BOSS, GROMACS, OpenMM or LAMMPS. Each solvent is BOSS's own united-atom model in a box of 512 molecules, made from BOSS 5.1's stored argon box; BOSS places the molecule and relaxes the box by Monte Carlo, and the density is compared with experiment.
Jorgensen, W. L.; Tirado-Rives, J. Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225–11236. doi:10.1021/ja9621760
LigParGen
Parameter generator
Free · on-site & command-line
An online front end to BOSS. Submit a molecule and the group's BOSS engine assigns its OPLS-AA atom types and computes its 1.14*CM1A or 1.14*CM1A-LBCC partial charges; the server returns the complete parameter set — bonds, angles, dihedrals and Lennard-Jones terms. Accepts SMILES, MOL and PDB input (up to 200 atoms) and outputs topologies for OpenMM, GROMACS, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. LigParGen Web Server: An Automatic OPLS-AA Parameter Generator for Organic Ligands. Nucleic Acids Res. 2017, 45, W331–W336. doi:10.1093/nar/gkx312
OPLS-AA/M
Force field
CHARMM & GROMACS
An improved OPLS-AA force field for proteins and RNA, with refined torsional energetics. Parameter and topology files are provided in CHARMM and GROMACS formats. Use requires geometric Lennard-Jones combining rules and 1,4 intramolecular nonbonded scaling.
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 (7). doi:10.1021/acs.jctc.9b00054
Conformer Energies
Calculator
Free · in-browser
An interactive OPLS-UA calculator for alkanes — straight-chain, branched, or cyclic. Enter a molecule as a SMILES string and get the energy-minimized relative energy of each distinct conformer: chain rotamers and ring puckers (chair, twist-boat, and beyond). Conformers are generated with RDKit and scored with the united-atom OPLS force field; the engine reproduces the conformer energies in Table 3 of the group's 2026 OPLS paper (n-alkanes and the cyclohexane/cycloheptane/cyclooctane series) to within ~0.25 kcal/mol.
Jorgensen, W. L.; Tirado-Rives, J. Free Energies of Solvation in Cyclohexane and Water: United-Atom vs All-Atom. J. Chem. Theory Comput. 2026, 22, 7581–7593. doi:10.1021/acs.jctc.6c00989
PDDG for MOPAC
Source patch
Free source code
FORTRAN 77 modifications that add the group's PDDG/PM3 and PDDG/MNDO semiempirical methods to MOPAC6, while retaining backward compatibility with the original package.