[gmx-users] SwissParam

[Michel Cuendet]

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 
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 !!


Best regards,

Michel Cuendet


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Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne
Switzerland
http://lausanne.isb-sib.ch/~mcuendet/
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