[gmx-users] Re: g_rmsf

bharat gupta bharat.85.monu at gmail.com
Wed Feb 9 06:52:54 CET 2011


Tsjerk,

Sorry for asking that .. actually I made a silly mistake while selecting
residues.. After plotting the graphs for common regions I found that first
100 amino acids shows a lot of fluctuations (compared to the one without any
loop insertion) ... Does the insertion caused a great change in the over
topology ... what could be the answer for this ?? ...

Is there any other way to check the effect loop insertion on the topology of
protein ... I heard of essential dynamics method and I asked u earlier about
the same .. u told me that 3ns time is small for such analysis but I have
found a paper (published in 1999) that has done ED analysis on a 1ns
simulated trajectory .. Whether doing such analysis for my data will be
acceptable ??

I also want to know how can I calculate the distance between two beta
strands (which are connected by a loop) ...

On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> We can't know that. We don't have your files (and we don't want them).
> Check what you did, and what index groups you have. Write out the
> structure for the index group and have a look. We're not a substitute
> for your brain here... :p
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta <bharat.85.monu at gmail.com>
> wrote:
> > Thanks for the advice and while creating the index file for first 100
> common
> > residues it found that both structures shows different no.of atoms. ..
> how
> > is that possible ??
> >
> > On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >>
> >> Hi Bharat,
> >>
> >> You can do it with post-processing the data you obtain from g_rmfs, if
> >> it's okay that the fit uses all residues in either case. Otherwise,
> >> you can make an two index files, including only the residues that are
> >> common to both.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta <bharat.85.monu at gmail.com>
> >> wrote:
> >> > I used the -res option ... and I got the rmsf in terms of residues but
> >> > still
> >> > the problem is that the two structures contain different amount of
> >> > residues
> >> > due to loop replacement in one structure.. In that case how shall
> >> > proceed to
> >> > check the effect of loop insertion on the overall topology of the
> >> > protein..
> >> > pls guide ??
> >> >
> >> > On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul <jalemkul at 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 <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
> >> >>>
> >> >>>    ========================================
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> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>> 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
> >> >>
> >> >> ========================================
> >> >> --
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> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> --
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> >
> >
> >
> > --
> > 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
> >
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
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
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