[gmx-users] protein-ligand interaction

[jalemkul at vt.edu]

Quoting ahmet y?ld?r?m <ahmedo047 at gmail.com>:

> Dear users,
>
> I want to investigate *Ligand effect *on the protein .
> To investigation the interaction of protein-ligand:
> *RMSD calculations:*
> 1.
> a) RMSD of Backbone
> b) RMSD of Backbone+ligand
> 2.
> a) RMSD of Protein
> b) RMSD of Protein+ligand
> 3.
> a) RMSD of Protein-H
> b) RMSD of Protein-H+ligand
> Which one would you recommend ( 1., 2., and 2.choice)?
>

Unless the effect of your ligand is very large (i.e., the whole  
protein is significantly more or less stable in the presence of the  
ligand), then likely none of these analyses will be particularly  
illustrative as they are not very sensitive to small changes.  You can  
get a per-residue RMSD by using g_rmsf -od to see the effect of the  
ligand on each residue.  Otherwise, the most common quantity measured  
is backbone RMSD.

-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

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