[gmx-users] Analysis of the RMSF of a ligand bound protein structure

PAULAMI CHATTERJEE chatterjee_paulami at yahoo.co.in
Thu Jul 16 10:46:32 CEST 2015

Dear all,
I am performing MD simulation on a ligand bound dimeric protein structure in Gromacs 5.04. For the calculation of RMSF of this dimeric protein I have used the following command
gmx rmsf -s md_0_1.tpr -f md_0_1_traj.xtc -res -o rmsf_res.xvgand selected 'C alpha' group.
But the resulting plot shows graph corresponding to the ligand also.

Is there any way to plot only the RMSF values of the dimeric protein without the bound ligand in gromacs? 
Will it be okay if I take the RMSF values of only the protein residues from rmsf_res.xvg and plot in any other graphical interface? 

Thanks and Regards,Paulami 

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