[gmx-users] re: LJ potential for Heme iron ???
nkyx at hotmail.com
Fri Oct 31 15:29:01 CET 2003
>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...
Maybe,someone else also met the same question as mine. see
The authors adopted the LJ parameters for Fe from Charmm because of the
collapse of free water.
> 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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