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All topologie and parameters to run MD simulation with Gromacs using the CHARMM force-field [Bjelkmar et al, J. Chem. Theory Comp, (2010)] are provided below. Parameters that could not be infered from the existing CHARMM force-field have been derived from MMFF using SwissParam [Zoete et al, J.Comp.Chem, (2011)].

For general information about Gromacs, please refer to


  • Download in the directory were the charmm forcefield files are located (typically $GMXDATA/gromacs/top/charmm27.ff/, where $GMXDATA is the environment variable defined in the GMXRC)
  • Replace the following files by the ones in SwissSidechain_gromacs/: aminoacids.rtp, aminoacids.hdb, gb.itp, ffbonded.itp, ffnonbonded.itp, atomtypes.atp. Warning: always copy the original files somewhere else before overwriting them.
  • Replace residuetypes.dat in $GMXDATA/gromacs/top/ by this file

D-amino acids

If you have several D-amino acids that are present in SwissSidecain in your structure, you can add these topology files to aminoacids.rtp and aminoacids.hdb, and this file to residuetypes.dat.