[gmx-users] rmsd between different monomers
Justin A. Lemkul
jalemkul at vt.edu
Sun May 9 13:29:25 CEST 2010
Anupam Nath Jha wrote:
>> 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....
It doesn't matter. The structure for calculation (-f) and the reference
structure (-s) are identical, so the RMSD has to be zero, regardless of the
fitting group and calculation groups chosen.
>>> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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