On 6/26/13 9:32 AM, aixintiankong wrote:
      Dear,
      when i keep the ligand in the active site,   I use the g_dist calculate  
the distance of two residues from two different loops. i look the sticks model 
of the two residues by pymol and find that there is a gap between the two 
residues. after using g_dist calculate the distance, i look the distance.xvg 
file and find that the |d|=0. why? In the pymol i can look the gap, but the 
distance.xvg show the |d|=0.

Have you verified that your index groups actually specify what you think they 
do?

      when i remove the ligand  and get the md.xtc, i calculate the distance 
between the two residues the |d|>1nm.
so i think the ligand can control the Channels opend, this is right or not ?

You have a potentially unreliable measurement involved, so I would not conclude anything. Beyond that, interpretation of the outcome is your task, based on your knowledge of the literature and the system at hand.

     And i only want to show teh |d| lines in the distance.xvg, how can i carry 
out it ?


That's the default behavior when plotting in XmGrace. You only get multiple sets plotted with the -nxy option.

-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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