[gmx-users] sulfate atomtype for ffgmx

[Justin A. Lemkul]

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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-- 
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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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