[gmx-users] protein-ligand interaction

[ahmet yıldırım]

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)?

Thanks
**

-- 
Ahmet YILDIRIM
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