[gmx-users] g__dist calculate the distance of two residues from different loops

[Justin Lemkul]

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

-- 
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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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