michel.cuendet at isb-sib.ch
Thu Oct 7 18:13:25 CEST 2010
Dear Gromacs users,
This is an announcement for 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
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 !!
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
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