File formats in Ligandbook¶

Ligandbook stores forcefield parameters in packages, which contain coordinates, topology information, and meta data. The meta data is stored in a database but the coordinates and topology data are stored in files. If the available file format is not appropriate for your code, try one of the force field conversion tools.

For a given molecule, a package contains the 3D structure of the compound in PDB format.

The "topology" data includes information on the bonds, angles, dihedrals, and improper dihedrals together with atom types and partial charges. Topologies are primarily stored in the ITP format as defined by the Gromacs simulation code. ITP files are validated for syntactic correctness. Other topology files such as AMBER TOP or CHARMM/NAMD PRM files may also be included in addition to an ITP file.