AMBER Archive (2005)

Subject: Re: AMBER: questions about MG ions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Sun Jul 31 2005 - 23:55:46 CDT

I ran a protein with a catalytic Zinc and two structural ions (another
Zinc and a Calcium). I had to use distance restraints for the
structural ions, but not the catalytic ion. I think this may be
because the catalytic Zinc was deeper in the protein (catalytic domain
portion of the protein was modeled) and the structural ions were near
the surface aiding in holding folds of the protein together. They may
have been better anchored if I had used the entire protein instead of
just the catalytic domain (however the domain was large enough to work
with!).

I'm not an expert in any fashion, just sharing my experience.

Kara Di Giorgio

On Jul 31, 2005, at 4:12 PM, JIANING WANG wrote:

> Hi, all,
>
> I have an pdb structure with Mg ion bound to two deprotonated Asp
> residues
> and nucleotide triphosphates. However, when I performed the
> minimization in
> Amber, Mg ions moved away from the original place. I saw some people
> suggestted using some distance constraints to the metal ions, but in
> my sense,
> if metal ions coordinate with some residues, it should not move even
> without
> constraint. Does anybody have such experience? How to deal with metal
> ions?
> Thanks in advance!
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