[gmx-users] rmsd between different monomers

Anupam Nath Jha anupam at mbu.iisc.ernet.in
Sun May 9 07:12:39 CEST 2010

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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