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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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