subarna thakur wrote:
Hello
I want to analyze the RMSF fluctuation of each residue of a protein
during a simulation run. I am giving the command
g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox
traj_avg.pdb. Then I am selecting the whole protein for the analysis. I
am getting the RMSF per atom in the .xvg file and I have to plot the
graph as RMSF versus atom no. but I want to have the RMSF of each amino
acid residue.How Can I get the RMSF of each residue , what is the
command for that?
Have you looked at g_rmsf -h? I suspect you'll find something useful.
-Justin
Subarna
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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