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).