[gmx-users] Regarding RMSD analysis result
naga sundar
naga25sundar at gmail.com
Tue Sep 25 09:22:32 CEST 2012
Dear justin
http://rmsdnagasundaram.blogspot.in/. This is the link to
my rmsd graph. Plz check it once and suggest me.
Thanks
On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım <ahmedo047 at gmail.com>wrote:
> Dear Tsjerk,
>
> You said "RMSD's above 1 nm are suspect, towards 2 highly likely not
> correct." What is the physical/biological/chemical meaning of what you say?
>
> Greetings
>
> 2012/9/24 Tsjerk Wassenaar <tsjerkw at gmail.com>
>
> > Hi,
> >
> > RMSD's above 1 nm are suspect, towards 2 highly likely not correct.
> > You have to make sure that the molecule is made whole before doing
> > RMSD analysis.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> > > You can also just quickly visualize it in VMD and see if anything your
> > looking at is not centred properly. If it isnt you just have to centre
> it.
> > >
> > > Stephan
> > >
> > > -------- Original-Nachricht --------
> > >> Datum: Mon, 24 Sep 2012 04:32:33 -0700
> > >> Von: naga sundar <naga25sundar at gmail.com>
> > >> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >> Betreff: Re: [gmx-users] Regarding RMSD analysis result
> > >
> > >> Dear justin
> > >>
> > >> Thanks for ur suggestions
> > >>
> > >> While speaking about periodic conditions, I
> > followed
> > >> the similar condition for both native and mutant complexes. For native
> > >> complexes not any big deviation was observed. So its confirmed that
> > >> nothing
> > >> wrong with periodic conditions. Since all the three mutations were
> > having
> > >> high clinical significance, we assuming mutation is the only reason
> for
> > >> this abnormal RMSD behavior. Sudden big increase in the RMSD was
> > observed
> > >> in previous mutational MD studies.
> > >> http://www.sciencedirect.com/science/article/pii/S0006291X08020792.
> > >>
> > >> Overall, all the factors are supporting our results. So shall we take
> > >> this
> > >> RMSD analysis as good result . Even after repeating the 20 ns MD
> > >> simulation
> > >> two times i got the same results.
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >>
> > >> >
> > >> >
> > >> > On 9/24/12 6:24 AM, naga sundar wrote:
> > >> >
> > >> >> Dear gromacs users
> > >> >>
> > >> >> We performed MD simulation analysis for native and
> > mutant
> > >> >> models of protein-protein complexes. From 20 ns simulation
> > trajectory,
> > >> we
> > >> >> generated RMSD graph for one native and three mutant complexes. For
> > >> native
> > >> >> complex in the entire simulation period, we observed a constant
> RMSD
> > >> >> (~0.15 to ~ 0.25 nm). But, three mutant complexes
> > >> >> showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We
> > >> analysed
> > >> >> all the 3D structure's in the fluctuated areas observed destruction
> > of
> > >> >> protein complexes.
> > >> >> All the three mutants were already experimentally analyzed and
> > reported
> > >> >> that they are involved in the destruction of protein-protein
> > >> interactions.
> > >> >>
> > >> >> Query 1: What may be the reason for sudden rise and fall of the
> RMSD
> > >> >> values
> > >> >> in mutant complexes. We are assume its because of the involvement
> of
> > >> >> mutation.
> > >> >> Query 2: Is there may any other reasons for drastic fluctuation in
> > the
> > >> >> RMSD
> > >> >> Query 3: Observed results are rite.
> > >> >>
> > >> >> Here iam attaching the RMSD graph for your observation.
> > >> >>
> > >> >>
> > >> >>
> > >> > Attachments to the list do not work. You will have to post a link
> to
> > a
> > >> > file sharing site if you wish to share an image.
> > >> >
> > >> > Such jumps in RMSD are very suspect. Since you are dealing with
> > >> > protein-protein complexes, accounting for periodicity can be very
> > >> > challenging. Have you properly fit the trajectory such that your
> > >> protein
> > >> > subunits are not jumping across periodic boundaries? If they are,
> > then
> > >> > your results are nothing more than an artifact. If they are not,
> then
> > >> you
> > >> > have something more interesting, but a tenfold increase in RMSD is
> > very
> > >> > peculiar.
> > >> >
> > >> > -Justin
> > >> >
> > >> > --
> > >> > ==============================**==========
> > >> >
> > >> > Justin A. Lemkul, Ph.D.
> > >> > Research Scientist
> > >> > Department of Biochemistry
> > >> > Virginia Tech
> > >> > Blacksburg, VA
> > >> > jalemkul[at]vt.edu | (540) 231-9080
> > >> >
> > >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >> >
> > >> > ==============================**==========
> > >> > --
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> > >>
> > >> --
> > >> Regards
> > >> N.NagaSundaram
> > >> --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> > post-doctoral researcher
> > Biocomputing Group
> > Department of Biological Sciences
> > 2500 University Drive NW
> > Calgary, AB T2N 1N4
> > Canada
> > --
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>
>
> --
> Ahmet Yıldırım
> --
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--
Regards
N.NagaSundaram
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