[gmx-users] Re: g_rmsf

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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 : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>         <mailto:monu46010 at yahoo.com <mailto:monu46010 at 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 at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at 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 : monu46010 at yahoo.com <mailto:monu46010 at 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

========================================