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

[Justin A. Lemkul]

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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