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

nk yx nkyx at hotmail.com
Wed Oct 29 10:52:01 CET 2003

>I never checked the actual LJ parameters of Fe. If they are zero, I
>don't have any other ones to give you, I'm afraid. But the heme and iron
>do behave properly as far as I can see, as do ligands bound close to it.
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.
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.

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