[gmx-users] Force Field Charge Parameters

[Nancy]

The OPLS-AA force field is used for glucose and trehalose in conjunction
with other force fields in the article by Sukit Leekumjorn and Amadeu K.
Sum:

"Molecular Dynamics Study on the Stabilization of Dehydrated Lipid Bilayers
with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), pp
10732–10740

Are you suggesting that the authors used incorrect parameters?


On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Nancy wrote:
>
>> Hello,
>>
>> I have successfully minimised and equilibrated two systems, one consisting
>> of a single molecule of ethylene glycol (1,2-ethanediol) in a water box, and
>> the other is one molecule of glycerol, also in a water box.  I am planning
>> to proceed to simulate other sugar alcohols (e.g. erythritol, arabitol,
>> mannitol, etc).  I used topolbuild 1.2 to generate topologies for ethanediol
>> and glycerol, and for the various atoms in these molecules, I used charge
>> values from methanol (the methanol tutorial included with GROMACS), i.e.
>> +0.398 for hydroxyl hydrogens, -0.574 for oxygens, and +0.176 for the
>> carbons.
>>
>>
> As I told you before, the origin of these charges, in the absence of some
> published validation of the parameters, is questionable at best.
>
>  Should I use these charge values for an arbitrary sugar alcohol, or should
>> I use the charge values specified in the article:
>>
>> "OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J.
>> Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.
>>
>>
> If you are using OPLS, probably yes.  But as I recall, you were running
> simulations with GROMOS96.  If this is the case, then using OPLS charges or
> other parameters is wholly inappropriate.  The simple fact is, you must use
> charges from the parameter set you intend to simulate, otherwise go through
> the laborious process of deriving them yourself.
>
>  Also, are there programs that will automatically generate charge values
>> and other parameters for an arbitrary molecule?
>>
>>
> There are several options, like the R.E.D. server or antechamber (available
> from the Amber folks), but be advised that you should always follow the
> methodology for whatever force field you're using.  If it's GROMOS (like
> you've been using before), neither of these approaches is necessary, and
> they may not give you correct parameters.  Read the primary literature and
> base your decisions on what you find.
>
> -Justin
>
>  Thank you.
>>
>> Nancy
>>
>>
>>
>>
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>>
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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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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