[gmx-users] sulfate atomtype for ffgmx
Mark.Abraham at anu.edu.au
Thu Dec 17 03:52:27 CET 2009
Niesen, Michiel wrote:
> Dear all,
> I would like to perform MD simulations on a molecule that contains a
> carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at
> the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur
> (S) and DMSO sulphur atomtypes are available. In literature I did find
> GROMACS simulations performed on systems with a sulfate group but all of
> them used the standard Sulfur atomtype.
> So my question; Would it be reasonable to use the sulfur atomtype for a
> sulfonyl group R-SO2-R? (as done previously in literature) If not, is
> there a sulfate atomtype available for ffgmx or would you recommend me
> to use another force field such as CHARMM for this system?
ffgmx is deprecated, so the answer is "use another force field". In
general it is not reasonable to use an atom type in a functional group
that differs markedly from that it which it was parameterized.
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