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<BR>
Thank you very much Justin<BR>
<BR>
On Mon, 02 Jun 2008 Justin A.Lemkul wrote :<BR>
>Quoting minnale <minnale_gnos@rediffmail.com>:<BR>
><BR>
> ><BR>
> > Thanks for your prompt reply to Erik and Florian<BR>
> > i have done according to Erik's reply but there is no change in the RMSD<BR>
> > values<BR>
> > iam mentioning what i have done<BR>
> ><BR>
> > 1.make_ndx -f protein.gro -o calpha_re20_90.ndx<BR>
> > selected 3 & r 20-90 ( 3 = calpha)<BR>
> ><BR>
> > this ndx gave input for g_rms<BR>
> > g_rms -f 7nsprot.xtc -n calpha_re20_90.ndx -pbc -s minwat -o rms_calpha.xvg<BR>
> > selected calpha_res20-90 for least square fit<BR>
> > selected calpha for RMSD<BR>
> > but there is no difference in RMSD values of protein, selected<BR>
> > protein&res20-90(index for segment) and calpha&res20-90(suggested one)<BR>
> ><BR>
> > have i made any mistake in mentioning options in commands<BR>
><BR>
>Yes, as Erik already mentioned, you must use the calpha_res20-90 group for both<BR>
>the fitting and the calculation. What you're showing is essentially the same<BR>
>thing you already showed in your previous message - you are calculating the<BR>
>RMSD of the entire 'calpha' group for the protein.<BR>
><BR>
>-Justin<BR>
><BR>
> ><BR>
> > Thanks in advance.<BR>
> ><BR>
> > On Mon, 02 Jun 2008 Erik Marklund wrote :<BR>
> > >minnale skrev:<BR>
> > >><BR>
> > >> Hi all,<BR>
> > >>I have run the protein in water for 7ns and plotted RMSD for whole protein<BR>
> > with 250 residues and segmented 70 residues out of 250 residues by using<BR>
> > index file, result in two cases values are nearly same and showing almost<BR>
> > same graph. I think it should be different in two cases.<BR>
> > >><BR>
> > >>the commands I have given for whole protein and segmented protein are<BR>
> > >><BR>
> > >>g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -o rms_whol7nsprot<BR>
> > >> selected c-alpha for least square fit<BR>
> > >> selceted c-alpha for RMSD calculation<BR>
> > >><BR>
> > >>g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -n 20_90res.ndx -o rms_segm7nsprot<BR>
> > >> selected 20_90res for least square fit<BR>
> > >> selected c-alpha for RMSD calculation<BR>
> > >><BR>
> > >>Any suggestions are appreciated<BR>
> > >>Thanks in advance<BR>
> > >><BR>
> > >><BR>
> > >><BR>
> > >>Swiss<BR>
> ><BR>
><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><BR>
> > >><BR>
> > >>------------------------------------------------------------------------<BR>
> > >><BR>
> > >>_______________________________________________<BR>
> > >>gmx-users mailing list gmx-users@gromacs.org<BR>
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> > >>Please search the archive at http://www.gromacs.org/search before posting!<BR>
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> > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> > >Hi,<BR>
> > ><BR>
> > >You have in fact calculated RMSD for all calphas in both cases, but only<BR>
> > used a subset of them for fitting in the second case. You need to create an<BR>
> > index group for the calphas in your segment and use that for your calculation<BR>
> > (and fitting).<BR>
> > ><BR>
> > >-- -----------------------------------------------<BR>
> > >Erik Marklund, PhD student<BR>
> > >Laboratory of Molecular Biophysics,<BR>
> > >Dept. of Cell and Molecular Biology, Uppsala University.<BR>
> > >Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
> > >phone: +46 18 471 4537 fax: +46 18 511 755<BR>
> > >erikm@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys<BR>
> > ><BR>
> ><BR>
><BR>
><BR>
><BR>
>========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul@vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>
><BR>
>========================================<BR>
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