Daggett Research Group | MMPL SchemaUniversity of Washington - College of Engineering - School of Medicine - Department of Bioengineering
We have developed an XML schema for standardizing, cataloging and sharing parameters and molecular definitions for molecular mechanics force fields. A graphical depiction of the entity relationship in the schema is available below. We have chosen to model the entities as effeciently as possibly opting for attributes over elements (e.g. for atomic parameters). The schema documents the fundamental atom types used by force fields in atom elements. Atoms are assembled into groups (e.g. methyl group) using group elements which are assembled into residue elements (e.g. amino acids, nucleic acids, lipids). Finally, residues are combined into molecules. At all levels above atoms, bond elements within the entities link atoms, groups and residues together to form larger chemical structures. Finally, parameter masks stored in bond, angle and torsion entities are applied to assembled molecules to determine intra-molecular potential parameters. We believe that parameter provenance is important, therefore, the schema begins with annotation elements for version, date, etc. and allows for liberal placement of comments and the inclusion of DOIs to track where specific parameters were published.
The molecular mechanics parameter library (MMPL) XML schema is available via the link below. The schema is subject to the BSD license and is copyright 2006-2009 by the University of Washington.
- David A. C. Beck
- Andrew Simms
- Valerie Daggett
Download the MMPL schema:
Page Created: July 24, 2009