[gmx-users] Re: g_rmsf
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 9 07:08:05 CET 2011
On 9/02/2011 4:52 PM, bharat gupta wrote:
> 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 ?? ...
Maybe the insertion does cause a change. Isn't that one of the things
you're trying to see? Maybe you've not got enough data. Maybe you've not
made a single-variable change. You have to have done a pair of
simulations (whose difference is known, well-defined and relevant) for
long enough time for the observables to converge within a simulation in
order to do a meaningful comparison of those observables across those
simulations.
> 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 ??
Computer power doubles about every 18 months. Things that were
too-short-but-acceptable a decade ago often will no longer be
acceptable. In the 80s people did vacuum MD with 0.7nm cutoffs, which
would be laughed at now.
> I also want to know how can I calculate the distance between two beta
> strands (which are connected by a loop)
Have a look at the short descriptions of the the tools in manual section
7.4 or 8, and then look up the detailed descriptions of useful-sounding
tools in the appendix.
Mark
> ...
>
> On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar <tsjerkw at gmail.com
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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>
> >> >>> <mailto: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>>
> >> >>> <mailto: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> <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>
> <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>
> >> >
> >> > --
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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 <mailto:monu46010 at yahoo.com>
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
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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 <mailto:monu46010 at yahoo.com>
>
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