[gmx-users] rmsd between different monomers
Anupam Nath Jha
anupam at mbu.iisc.ernet.in
Sun May 9 12:52:21 CEST 2010
> 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.
but I am giving different groups (as chains). I am trying to get RMSD between
two monomers in same structure so what's wrong in that....
>> 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 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
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Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and a collection of facts is not
Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
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