Alok Jain wrote:
Hi,
I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,
1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for the selected monomer CA
atoms.
g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx
2. I calculate RMSF for the complete protein CA atoms
g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg
I find the output from these to commands for the same monomer A
residues are different. The second command calculates a very high RMSF
for the same residues.
Why is it so ?? Or am I making a mistake at some place ??
The selected index group has a least-squares fit performed on it. If the
fitting group is different, the output RMSF will be different. In case (1)
you're doing the fitting and establishing a reference for RMSF from just one
monomer and then doing the calculation on that group. In case (2) you're using
the whole protein for the calculation.
-Justin
Thanks in advance.
Alok
--
========================================
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
========================================
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