Dear CHARMM users,
The Molecular modeling Group of the Swiss Institute of Bioinformatics is pleased to inform you that the SwissParam web server is now open:http://www.swissparam.ch
This service provides topologies and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
The server is fully automatic, and the user only needs to provide the organic molecule of interest in the mol2 format.
The mol2 file must contain all atoms, including hydrogens, and correct 3D coordinates.
Topology and parameter files are sent to the user by e-mail, generally within minutes.
The parameters 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.
This service is free for academic use. A CHARMm license is required for users from private companies.
The SwissParam approach to derive rapidly topologies and parameters for small organic molecules is also used by the SwissDock docking web service that we opened recently (swissdock.vital-it.ch). SwissDock uses EADock, our docking software based on the CHARMM force field:http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24007
The success rate of the docking approach, using the SwissParam parameters, is close to 75 %, illustrating the relevance SwissParam for such applications.
Please, note that, although SwissParam is working properly, the service is in beta version.
In case of problem, or if you'd like to send us some feedback, don't hesitate to contact us.