[gmx-users] sulfate atomtype for ffgmx

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 17 03:52:21 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.

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.


> Kind regards,
>  Michiel
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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