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

[minnale]

Thank you very much Justin

On Mon, 02 Jun 2008 Justin A.Lemkul wrote :
>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
> >
><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2133997_2126411/2134144/1?PARTNER=3&OAS_QUERY=null>
> > >>
> > >>------------------------------------------------------------------------
> > >>
> > >>_______________________________________________
> > >>gmx-users mailing list    gmx-users at gromacs.org
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > >>Please search the archive at http://www.gromacs.org/search before posting!
> > >>Please don't post (un)subscribe requests to the list. Use the www interface
> > or send it to gmx-users-request at gromacs.org.
> > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >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
> > >
> >
>
>
>
>========================================
>
>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/
>
>========================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080603/1ffbaef5/attachment.html>