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

[Justin A. Lemkul]

Niesen, Michiel wrote:
> 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.
> 

That's a bit odd, of all the force fields distributed with Gromacs, ffgmx has 
among the fewest available atom types, many of which have been improved upon in 
later versions of Gromos96.

> 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.

Parameters for sugars and heme are available in several of the Gromos96 
parameter sets (I certainly found them with a quick look through the ffG53a6 
files), so surely there are parameters for those atom types.  Although, indeed, 
there is only one sulfur atom type, generic sulfur.  Has no one done simulations 
with sulfate?  I know I have seen papers reporting (at least) SDS parameters 
that may give you a starting point.

> 
> 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?
> 

The general advice (and there was a lengthy discussion about this some time ago) 
is that ffgmx should not be used.  It is sort of a mix of several different 
parameters with some modifications that are not well-documented.

If parameters have been published for your species under OPLS-AA, it should be 
trivial to incorporate them into the existing ffoplsaa* files.  That's one of 
the nice features of Gromacs - if you have parameters for any force field, you 
can use them for your simulations :)

-Justin

-- 
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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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