[gmx-users] rmsd between different monomers

[Justin A. Lemkul]

Anupam Nath Jha wrote:
> 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
> 

In the command you've given (with the same file for -s and -f), you're computing 
the RMSD at time zero, after fitting to the structure at time zero, so the RMSD 
must be zero.

> 
> so the rmsd = 0.0000001
> 
> whereas when I use online server it gives me 1.4.
> 
> so what am I doing wrong?
> 

Then whatever you're giving the online server is different.  The Gromacs 
calculation seems to be correct.

-Justin

> regrads
> anupam
> 
> 
> 

-- 
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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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