This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
Created and maintained by the Molecular modeling group
The data are derived from the Merck Molecular ForceField (MMFF). Dihedral angle terms are taken as is, while only the harmonic part of the bond, angle and improper terms are retained. Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22.
These parameters are intended for "drug design" type calculations, like docking, minimizations, rapid binding energy estimation (LIECE), etc... Deeper parameterizations are required for applications in which a very fine description of the molecule is required, (e.g. normal mode calculations...). SwissParam results can then be used as a starting point for such a procedure.
SwissParam is automatically used by SwissDock
, a web server for docking small molecules to proteins.
This server is free for academic use. A CHARMm license is required for users from
If you are using SwissParam, please, cite:
V. Zoete, M. A. Cuendet, A. Grosdidier, O. Michielin, SwissParam, a Fast Force Field Generation Tool For Small Organic Molecules
, J. Comput. Chem, 2011, 32(11), 2359-68. PMID: 21541964
, DOI: 10.1002/jcc.21816.
List of papers citing SwissParam
- How to obtain a correct mol2 file for use with SwissParam.
- How to use SwissParam to setup a molecular dynamics simulation of a protein with a small-molecule ligand in GROMACS using the CHARMM forcefield.