[gmx-users] Re:re: LJ potential for Heme iron ???
feenstra at chem.vu.nl
Thu Oct 30 10:07:05 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...
> 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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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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