[gmx-users] LJ potential for Heme iron ???

[Martina Bertsch, PhD]

>  The iron non-bond parameters are available at the AutoDock web site:
>
> http://www.scripps.edu/pub/olson-web/doc/autodock/parameters.html#PARAMETERS 
>
>
> The parameters are derived from two different force fields, AMBER 
> (1986) and the Merck FF, MMFF [T. A. Halgren, (1992), "Representation 
> of van der Waals (vdW) Interactions in Molecular Mechanics Force 
> Fields: Potential Form, Combination Rules, and vdW Parameters", JACS, 
> 114, 7827-7843]. The combined AMBER (1986)/MMFF parameters represent a 
> new and untested set of parameters, so they should be used with caution.
>
> Look for the table with the
>
>Rij, epsij, C12, C6
>
> values. The AutoDock convention requires one-letter element symbols; 
> therefore, iron is " f ".
>
> Kind regards,
>
> Martina Bertsch, Ph.D.
> Northwestern University
> Feinberg School of Medicine
> Molecular Pharmacology and Biological Chemistry
> 303 East Chicago Avenue
> Chicago, IL 60611
>
>
> Anton Feenstra wrote:
>
>>nk yx wrote:
>>
>>>Yes, the simulation goes well when a ligand is close to the heme.
>>>But when the protein has no ligand, the free water is easy to collapse 
>>>nearby the heme.
>>>
>>
>>Strange. I have also simulated a P450 without ligand, which had water
>>in the active site instead. That didn't give any problems that I saw...
>>
>>>I found the parameters(different to zero) for Fe2+ in OPLS force field. 
>>>Might I use the parameters for the Fe since I modified the charge from 
>>>+2 to +1.
>>>
>>
>>That would at least be a good initial guess, I think.
>>
>>
>

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