rossen at kth.se
Fri Oct 8 02:21:11 CEST 2010
Thanks for contributing!
I added a page about it on the Gromacs website:
On 10/7/10 7:13 PM, Michel Cuendet wrote:
> SwissParam, 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:
> 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
> 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 !!
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