[gmx-users] Re:re: LJ potential for Heme iron ???

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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