Thanks for contributing!
I added a page about it on the Gromacs website:
http://www.gromacs.org/Downloads/Related_Software/SwissParam
Rossen
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:
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 !!
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