try -res option On Wed, Feb 9, 2011 at 08:51, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > bharat gupta wrote: > >> Actually after loop incorporation I want to check which region of the >> protein shows much deviation , which I think can be done by plotting rmsf >> values from both proteins.. but the problem here is that one structure which >> contains loops has more no. of atoms as compared to other str. without loop >> insertion .. so which way it can be analyzed ?? >> >> Also g_rmsf gives RMSF values for atoms of residues but not of residues >> how can I get the values for residues .. >> > > Please read g_rmsf -h. > > -Justin > > Pls help ?? >> >> >> On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> bharat gupta wrote: >> >> Hi, >> >> I want to calculate the RMSF of residues and not of protein ... >> how can this be done with g_rmsf.. >> >> Also I want to see the rmsf of certain residues .. for which I >> created the .ndx file containint those residues only .. and >> after using g_rmsf with index file gives the RMSF for whole >> protein backbone and not for that index file residues ... what >> shall I do to have RMSF of index file residues ?? >> >> >> The default output of g_rmsf is a plot of RMSF (of each residue) vs. >> residue. No index file is required to obtain this, unless you want >> to do the fitting to some custom group. Is this not what you want? >> >> -Justin >> >> -- Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> >> <mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>> >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- * --------------------------------- Thanks and regards Bipin Singh * * *
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