Quoting ahmet y?ld?r?m <ahmedo...@gmail.com>:
Dear Justin,
You said " You can get a per-residue RMSD by using g_rmsf -od to see the
effect of the ligand on each residue."
1. Can you explain the difference between what goes into the -o file, and
what goes into the -od file?
The -o output is RMSF; the -od output is RMSD.
2. How should I create a index file to see the effect of the ligand on each
residue? Do I have to create the index file?
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg
Is this command sufficient to see the effect of the ligand on each residue?
An index file should not be necessary. By default, the output is per
atom, so use the -res flag if you want the measurements averaged over
all atoms in each residue. The command is sufficient to measure the
RMSD per residue. Whether or not that is sufficient is up to you.
3. Furthermore, can you suggest the other analysis tools to see the effect
of the ligand *on protein*?
You should identify the quantities you wish to measure, then read in
the Gromacs manual about the different utility programs available.
You'll learn far more that way.
-Justin
Thanks in advance
2011/5/28 <jalem...@vt.edu>
Quoting ahmet y?ld?r?m <ahmedo...@gmail.com>:
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)?
Unless the effect of your ligand is very large (i.e., the whole protein is
significantly more or less stable in the presence of the ligand), then
likely none of these analyses will be particularly illustrative as they are
not very sensitive to small changes. You can get a per-residue RMSD by
using g_rmsf -od to see the effect of the ligand on each residue.
Otherwise, the most common quantity measured is backbone RMSD.
-Justin
--
========================================
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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Ahmet YILDIRIM
--
========================================
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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