[gmx-users] the effect of the ligand on each residue

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> Thanks for your reply. Well, to explore the effect of the ligand on protein
> 
> g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg
> Select a group: 1
> Selected 1: 'Protein'
> Select a group: 13
> Selected 13: 'LİGAND'
> 
> Does this choice make sense?
> 

Whether or not anything makes sense is up to you.  You have to interpret the 
data you get for your system.  The command is sound, so you probably got output. 
  But as for the applicability or whether or not it makes sense to do this 
analysis is, again, entirely up to you.

-Justin

> 
> 30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> yazdı:
> 
> 
> 
>     ahmet yıldırım wrote:
> 
>         Dear users,
> 
>         I want to see the effect of the ligand on each residue using the
>         following command:
>         g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
> 
>         Select group(s) for root mean square calculation
>         Select a group: ?
>         Which group should I choose?
> 
> 
>     The group that is most meaningful to you, based on the behavior
>     observed in the trajectory.  You can analyze backbone, sidechain, or
>     all protein atoms separately.  Several iterations may be
>     informative, using several different groups.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> 
> -- 
> Ahmet YILDIRIM

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================