[gmx-users] how to distancing the counter ions from the protein?

[Justin A. Lemkul]

jayant james wrote:
> well it seems to be on the protein's surface is it OK?
>
What command did you issue?  Random placement of ions can sometimes lead 
to ions being placed in unhappy places, in which case you can just run 
genion again with a different random seed.  If you told genion to place 
ions at the most electrostatically-favorable locations, it wouldn't 
surprise me that ions would be placed close to charged residues.

But I guess it all depends on your evaluation of "too close."

-Justin

> On Mon, Jun 9, 2008 at 6:08 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     jayant james wrote:
>
>         Hi!
>         I had to incorporate a salt conc of 0.15M NaCl and once I have
>         them in put in the the box,via genion, I find that they are in
>         close proximity to the protein. Is it possible to keep them
>         away from the protein because I do not want them so close !!
>
>
>     What about your system makes "close proximity" seem wrong?
>
>     Mark
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>
>
> -- 
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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