[gmx-users] protein-ligand interaction
Justin A. Lemkul
jalemkul at vt.edu
Mon May 30 00:25:46 CEST 2011
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 <ahmedo047 at gmail.com
> <mailto:ahmedo047 at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
> Quoting ahmet y?ld?r?m <ahmedo047 at gmail.com
> <mailto:ahmedo047 at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
> Quoting ahmet y?ld?r?m <ahmedo047 at gmail.com
> <mailto:ahmedo047 at 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> Please don't post (un)subscribe requests to the list.
> Use thewww interface
> or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list