ahmet yıldırım wrote:
Dear users,
I am getting pairs of values in the output files as I said before. What
is this mean? Furthermore, though my system have 451 residue, it seems
as 230 residue ( and 1th residue does not seem in the out files). What
could be the problem?
It looks like you have two separate chains.
-Justin
*_
output file:_*
# This file was created Sun May 29 22:33:05 2011
# by the following command:
# g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
#
# g_rmsf is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "RMS fluctuation"
@ xaxis label "Residue"
@ yaxis label "(nm)"
@TYPE xy
2 0.1217
3 0.0952
4 0.0760
5 0.0740
6 0.0613
7 0.0565
.............
227 0.0785
228 0.0955
229 0.1254
230 0.1352
2 0.1181
3 0.0851
4 0.0713
5 0.0674
6 0.0645
7 0.0631
8 0.0707
9 0.0699
........
228 0.1034
229 0.1161
230 0.1206
29 Mayıs 2011 19:28 tarihinde ahmet yıldırım <ahmedo...@gmail.com
<mailto:ahmedo...@gmail.com>> yazdı:
Dear Justin,
I used -res flag with the following command but I get pairs of
values in the output files. is there any mistake related with the
command I used?
g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res
2011/5/29 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Quoting ahmet y?ld?r?m <ahmedo...@gmail.com
<mailto: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 <mailto:jalem...@vt.edu>>
Quoting ahmet y?ld?r?m <ahmedo...@gmail.com
<mailto: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 <http://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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Ahmet YILDIRIM
--
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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