[gmx-users] rmsd between different monomers

[Itamar Kass]

Hi Anupam ,

To me it seems that you have used the the wrong groups for the RMSD, you
actually compare the protein to himself. Have a second look on at the
group contact, you groups should be numbered 12 or higher.


cheers,
Itamar

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at med.monash.edu.au
============================================

----- Original Message -----
From: Anupam Nath Jha <anupam at mbu.iisc.ernet.in>
Date: Sunday, May 9, 2010 3:48 pm
Subject: [gmx-users] rmsd between different monomers
To: gmx-users at gromacs.org

> 
> Dear all
> 
> I made an index file with 4 different groups for 4 different chains 
> (since my
> protein is a tetramer) and then run
> 
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
> 
> to get the rmsd between two different monomers from the same 
> structure,it asked me two different groups and I gave 0 and 1.
> 
> The output file is like this
> 
> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
> #
> # g_rms is part of G R O M A C S:
> #
> # Grunge ROck MAChoS
> #
> @    title "RMSD"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "RMSD (nm)"
> @TYPE xy
> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
>   0.0000000    0.0000001
> 
> 
> so the rmsd = 0.0000001
> 
> whereas when I use online server it gives me 1.4.
> 
> so what am I doing wrong?
> 
> regrads
> anupam
> 
> 
> 
> -- 
> 
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
> 
> 
> 
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