AMBER Archive (2003)

Subject: Re: Question: Nmode with counter ions.

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 24 2003 - 18:16:22 CDT

On Thu, Apr 24, 2003, Masaki Tomimoto wrote:
>
> I am going to perform N-mode a protein (~ 250 a.a.) which contains Mg2+
> inside the protein (it is seen X-ray crystallographically), and is given two
> Cl- for electrostatic neutralization by leap. My question is, (1) shall we
> keep both ions in N-mode, (2) shall we keep only Mg2+ in N-mode, (3) shall
> we ignore all ions, (4) other suggestion.
>

It depends on what you are going to do with the results, and how tightly
bound the ions are.

It would almost never be desirable to include mobile counterions for normal
modes: these atoms don't have any "equilibrium position" as requried for
that sort of analysis.

If the magnesium are tightly enough bound to be considered "part of the
molecule" (e.g. they are there whether or not other ligands/cofactors are
bound, etc.) then you could include them. Remember that a single normal
mode calculation is usually not very helpful; you usually need to be comparing
two different but similar states (as in mm-pbsa, for example). For such
comparisons, the magnesium ions must be present in both calcualtions, or in
neither, in order to consistent.

..hope this helps...dac 

-- 

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