From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Oct 06 2005 - 20:21:20 CDT
1) After. Autoionize chooses the positions of the ions based on water
molecules (it removes a water molecule for each ion placed).
2) Autoionize is trying to satisfy two constraints: neutralizing the
system and matching the desired concentration. However, if your system
size is small, it only requires a few ions to match the concentration.
But your charge is so large that it requires a lot of Na+ just to
neutralize it! Unfortunately, you only have two courses of action:
increasing your concentration until you get a mix of charges (but
possibly going beyond physiological conditions) or increasing your
system size. Although, I think, for most purposes you won't really
need the chloride ions unless you know they are important to the
function of what you are studying.
3) I'm not a biologist by training, so I can't say with certainty, but
that range seems reasonable (I think I've seen in the literature
100-150 mM before).
On Oct 6, 2005, at 6:36 PM, Shirley Li wrote:
> Thanks a lot.
>
> I have some further THREE questions:
>
> 1) Should ions be added AFTER or BEFORE the protein is
> solvated?
>
> 2) The protein is -36e charged. I tried to add ions
> after solvating the protein, using the following
> command from autoionize:
> autoionize -psf file_wb.psf -pdb file_wb.pdb -is 0.05
> -o file_ion
>
> I got a warning as follows, even though I tried "-is
> 0.2":
>
> WARNING: ion concentration too low, cannot add Cl
> ions!
> Adding 36 Na and 0 Cl ions, total 36 ions
>
> Could sb tell me this is an important issue, and how
> to solve it?
>
> 3)I got to know that ion concentration should be in
> the range 1–200 mM, is it correct?
>
> Your help will be greatly appreciated.
>
> Shirley
>
>
>
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