[gmx-users] Re: sulfate atomtype for ffgmx (Justin A. Lemkul)

Niesen, Michiel mniesen at coh.org
Thu Dec 17 20:54:48 CET 2009

Thank you both for the suggestions. 

My system does also contain carbohydrates (sugar) and ffoplsaa.atp does not contain the atomtypes for these molecules. Even though carbohydrate parameters have been published for OPLS they are not present in the ffoplsaa.atp file. I did look into the available atomtypes in all the force fields in the downloaded GROMACS package (4.0.5) and the one that has most of the molecules I require is ffgmx. 

Perhaps the GROMOS force fields can be used as well allthough they dont have seperate sugar atomtypes (CH2 = aliphatic or sugar carbon), or the porphyrin N that is also present in my simulation. The Sulfate is also missing in GROMOS.

That was the reason why I finally ended up with the decrapetated ffgmx, because it contains all but one specific atomtype I require. Should I prevent using ffgmx completely since it is decrapetated? Can the OPLS-AA carbohydrate parameters be ported to GROMACS? Or is it better to try and run my system in a different MD package that contains all specific atomtypes?



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


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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