[gmx-users] Same values are showing when tried to plot rmsd

[Justin A. Lemkul]

Quoting minnale <minnale_gnos at rediffmail.com>:

>
> Thanks for your prompt reply to Erik and Florian
> i have done according to Erik's reply but there is no change in the RMSD
> values
> iam mentioning what i have done
>
> 1.make_ndx -f protein.gro -o calpha_re20_90.ndx
>  selected 3 & r 20-90 ( 3 = calpha)
>
> this ndx gave input for g_rms
> g_rms -f 7nsprot.xtc -n calpha_re20_90.ndx -pbc -s minwat -o rms_calpha.xvg
>   selected calpha_res20-90 for least square fit
>   selected calpha for RMSD
> but there is no difference in RMSD values of protein, selected
> protein&res20-90(index for segment) and calpha&res20-90(suggested one)
>
> have i made any mistake in mentioning options in commands

Yes, as Erik already mentioned, you must use the calpha_res20-90 group for both
the fitting and the calculation.  What you're showing is essentially the same
thing you already showed in your previous message - you are calculating the
RMSD of the entire 'calpha' group for the protein.

-Justin

>
> Thanks in advance.
>
> On Mon, 02 Jun 2008 Erik Marklund wrote :
> >minnale skrev:
> >>
> >>  Hi all,
> >>I have run the protein in water for 7ns and plotted RMSD for whole protein
> with 250 residues and segmented 70 residues out of 250 residues by using
> index file, result in two cases values are nearly same and showing almost
> same graph. I think it should be different in two cases.
> >>
> >>the commands I have given for whole protein and segmented protein are
> >>
> >>g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -o rms_whol7nsprot
> >>   selected c-alpha for least square fit
> >>   selceted c-alpha for RMSD calculation
> >>
> >>g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -n 20_90res.ndx -o rms_segm7nsprot
> >>   selected 20_90res for least square fit
> >>   selected c-alpha for RMSD calculation
> >>
> >>Any suggestions are appreciated
> >>Thanks in advance
> >>
> >>
> >>
> >>Swiss
>
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> >>
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> >Hi,
> >
> >You have in fact calculated RMSD for all calphas in both cases, but only
> used a subset of them for fitting in the second case. You need to create an
> index group for the calphas in your segment and use that for your calculation
> (and fitting).
> >
> >-- -----------------------------------------------
> >Erik Marklund, PhD student
> >Laboratory of Molecular Biophysics,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596,    75124 Uppsala, Sweden
> >phone:    +46 18 471 4537        fax: +46 18 511 755
> >erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
> >
>



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Justin A. Lemkul
Graduate Research Assistant
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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