Feature List

User Interface

  • Submission of molecules with molecular drawer, SMILES or PDB file.

  • Search a database of pre-calculate molecules with various descriptors including 3D structures. ref:

  • Links molecules in other databases including CheMBL, RCSB PDB, and ChemSpider.

  • Save molecules of interest

  • Provision of an API for automated access to the database (on request).

  • Tools to visualize and compare parameters for molecules submitted in alternative conformations and for users to flag problems with specific molecules.

  • A tool to match and reorder PDB files for identical molecules with alternative atom names and/or atom order: PDB Match and Reorder.

Parameter Generation

  • Lennard Jones parameters refined against experimental solvation and pure liquid properties.

  • ATB parametrisation and validation is performed using a single-range 1.4 nm cutoff for both Lennard Jones and Coulomb interactions (see FAQ)

  • Atomic charges fitted to QM electrostatic potentials at B3LYP/6-31G* level of theory (for molecules < 50 atoms).

  • Robust symmetry routines to ensure identical parameters are assigned to chemically equivalent atoms, bonds and angles.

  • Bonded parameter assignment using force constants estimated from Hessian (B3LYP/6-31G*, for molecules < 40 atoms).

Automated Calculation Pipeline

  • Automated QM calculation pipeline with error recovery (low failure rate).

  • Automated QM and MM energy minimised structure comparison.

  • Automated calculation of solvation free energies (restricted).

Output Formats

  • GROMACS (GROMOS 54A7).

  • GROMOS96 (GROMOS 54A7).

  • GROMOS11 (GROMOS 54A7).

  • LAMMPS (GROMOS 54A7).

  • APBS (Adaptive Poisson-Boltzmann Solver) file format (.pqr).

  • CNS (Crystallography & NMR System).

  • CCD CIF (compatible with the Phenix, CCP4, Refmac5 and CYANA X-ray and NMR refinement packages).

  • eLBOW CIF (compatible with the Phenix X-ray refinement packages).

  • An extended and generalized mmCIF format incorporating a complete description of all force field parameters including units.

  • AMBER via a tool to convert GROMOS system topology files (.top) to the AMBER format (.prmtop).