[gmx-users] rmsd between different monomers
Itamar.Kass at med.monash.edu.au
Sun May 9 09:09:44 CEST 2010
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.
"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
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----- 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?
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> Ph. no.-22932611
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