Suppose if I want to get the RMSD plot of animo acids of an active site of the proteins only, how can I get it using the GROMACS 4.5.6 version? What will the command be, and how should it be written?
I am just a beginner in molecular dynamic simulation. Can you tell me how can I make that ndx file for active site residues. Can you tell the command if I have 3 amino acid residues such as CYS23, HIS56 and ASP128. Please Sir help me