Gromacs

SwissParam

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    SwissParam is a web service that provides topologies and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with the CHARMM or GROMACS softwares:

    http://swissparam.ch/

    The server is fully automatic, and the user only needs to provide the organic molecule of interest in the mol2 format. Topology and parameter files are sent back by e-mail, generally within minutes. For GROMACS users, an itp file is generated for the small molecule, which must be included to the protein or DNA topology produced by GROMACS. A tutorial page explains step by step how to set up a protein-ligand system.

    Force field 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 (the quartic part is discarded). Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22.

    The service is intended for fast and easy force field generation. The parameters have been tested in "drug design" type of calculations, like docking, minimizations, rapid binding energy estimation (LIECE, MMGB/SA), etc... Deeper parameterizations are probably required for applications in which a finer 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.

    Enjoy SwissParam, and please notify us of any question or suggestion for improvement. Try SwissParam now !!

    Page last modified 00:19, 8 Oct 2010 by rossen