Swiss Institute of Bioinformatics
Don't know where to start?
Try with an example
1 - Submit the query molecule
Upload a Mol2 file
(only 1 molecule, with all hydrogens and 3D coordinates)
If the H atoms are not present, the parameterisation will possibly choose a default protonation state and rename the atoms.
Hide the sketcher
You submitted a Mol2 file. The latter will be treated as is, and atom naming will be kept when possible. However, if you modify the molecule in the sketcher, the atom naming and the molecular conformation provided in the Mol2 file will not be use during the parameterization.
No SMILES available?
Draw a molecule
using the sketcher
2 - Select approach
Data are derived from the Merck Molecular Force Field (MMFF). Dihedral angle terms as taken as is, while only the harmonic part of the bond, angle and improper terms are retained. Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM36.
Multipurpose atom-typer for CHARMM (MATCH) approach, the data are derived from CHARMM General Force Field. Atom-types are assigned by a general chemical pattern-matching engine. Charges and force field parameters are assigned compared to a list of chemical fragments.
MMFF-based + MATCH
3 - Launch parameterization
(Provide a query molecule before submitting)
obtain a correct Mol2 file for use with SwissParam
use SwissParam to setup a molecular dynamics simulation of a protein with a small-molecule ligand in GROMACS using the CHARMM force field
This Web tool is operated by the
Molecular Modelling Group
University of Lausanne
SIB Swiss Institute of Bioinformatics