[gmx-users] rmsd between different monomers

Sun May 9 14:46:05 CEST 2010

you said you have used online server for superimposition ...
which one you used...
try TOPMATCH server....

On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha <anupam at mbu.iisc.ernet.in>wrote:

>
> Ok.
>
> But when I run this command
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>
> it ask me groups... and that i thought is for fitting///
>
> for example -
>
> ------------------------
> Select group for least squares fit
> Group     0 (C-alpha_chain1) has   249 elements
> Group     1 (C-alpha_chain2) has   249 elements
> Group     2 (C-alpha_chain3) has   249 elements
> Group     3 (C-alpha_chain4) has   249 elements
> Select a group: 0
> Selected 0: 'C-alpha_chain1'
> Select group for RMSD calculation
> Group     0 (C-alpha_chain1) has   249 elements
> Group     1 (C-alpha_chain2) has   249 elements
> Group     2 (C-alpha_chain3) has   249 elements
> Group     3 (C-alpha_chain4) has   249 elements
> Select a group:1
> Selected 1: 'C-alpha_chain2'
>
> ---------------------------------
>
> Is it not superimposing these two chins and calculating RMSD between
> them???
>
> --
> anupam
>
>
> > On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:
> >>
> >>
> >> 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.
> >
> > Exactly. Only if you can fit group A from one file to group B from a
> > file (which may or may not be the same file) can Anupam do this
> > calculation. g_rms seems not to allow this.
> >
> > Instead, Anupam should use trjconv or editconf to select groups
> > beforehand, as I think I suggested a few days back. Thus (say) editconf
> > produces file_with_group_A.pdb and editconf produces
> > file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s
> > file_with_group_B. This will work if the two groups have the same atoms
> > in matching orders, which should be the case for a tetramer setup.
> >
> > Mark
> >
> >>>>> 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
> >>>>>
> >>>>>
> >>>>>
> >>>> --
> >>>> ========================================
> >>>>
> >>>> 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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> >>>>
> >>>
> >>>
> >>
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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
> necessarily science.
>
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
>
>
>
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-- 
Bharath.K.Chakravarthi
Ph:9535629260
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