All topologie and parameters to run MD simulation with Gromacs using
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)].
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
Replace residuetypes.dat in $GMXDATA/gromacs/top/ by this file
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.