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.
If there is precedent, you may be able to use it. However, you should be warned
that ffgmx is considered a deprecated force field, and in the absence of a very
compelling reason to use it, probably isn't a wise choice. There are many
(newer) versions of Gromos force fields that are probably more reliable.
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?
There are numerous sulfur atom types in OPLS-AA that may be usable. Have a look
at the .atp file to see. CHARMM is not yet officially supported in Gromacs, so
that force field probably isn't a viable option.
-Justin
Kind regards,
Michiel
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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