[gmx-users] LJ potential for Heme iron ???
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Thu Oct 30 22:13:01 CET 2003
> The iron non-bond parameters are available at the AutoDock web site:
> 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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