Re: [AMBER] Help building a model of a 2F-2S protein with

From: Pengfei Li <>
Date: Mon, 3 Feb 2020 21:02:20 -0500

Hi Gustavo,

In order to make recognize the Fe ions, you should put each Fe ion into a separate residue.

For the two S atoms, you can put them either into one residue or into two separate residues. I would suggest you to put them into two separate residues for this case, which may a more clean way to handle the system.

Hope it helps,

> On Jan 29, 2020, at 1:57 PM, Gustavo Seabra <> wrote:
> Hi all,
> I am trying to follow the tutorial here
> <>, and apply
> the procedure to a protein of interest in my group here. The tutorial
> itself is very clear and well written (thanks!). however, the question
> arises when trying to apply to my system.
> The point is that I’m trying to parametrize a 2F-2S system, where the Fe
> atoms are connected to the protein by 3 Cysteines, leaving the 4th valence
> open for a ligand, like this:
> [image: image.png]
> My question is: in the tutorial, the metal atoms get separated in one
> residue for each metal atom, this residue containing just this metal atom,
> by itself. This is straightforward in the case of one metal atom connected
> to protein residues. However, how should I consider it here? Should I
> separate each Fe atom in its own residue? And in this case, how to deal
> with the S atoms? (I already parametrized the ligand.)
> I could not find examples with similar sites. I found this article here
> <>, but unfortunately they
> don’t provide any details on how the site was prepared, only mention that
> they used MCPB… (Yes, I looked into the supplemental information… nothing
> there either L)
> Thanks a lot for any help you can give on this issue!
> All the best,
> --
> Gustavo Seabra.
> <image.png>_______________________________________________
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Received on Mon Feb 03 2020 - 18:30:02 PST
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