On 11/19/12 11:50 AM, shch406 wrote:
I would have chosen the groups in the opposite manner. You're interested in
the
presence of water around the chosen arginine residue, not the presence of
arginine around water, right? Given this order of chosen groups, the RDF
seems
to make sense (very low probability that arginine is close to all water
molecules), though it doesn't represent what you likely want.
-Justin
Of coarse, I'm interested in the presence of water around the arginine.
But I did reverse order of groups, i.e. I toke water as the "1 group" and
arginine sige
chain tip as the "reference group", however have obtained absolutely the
same curve.
May be there exist some peculiarity in using g_rdf dialog to select groups?
I've never had an issue with similar commands. Can you provide us with your
full g_rdf command line? Have you verified that the index group for the
arginine residue is correct? Can you provide a link to an image of the
resulting RDF?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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