Thank you Jason,
for your explanation...
On Thu, Oct 7, 2010 at 6:38 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Oct 7, 2010 at 12:42 AM, hirdesh kumar <hirdeshs8.gmail.com>
> wrote:
>
> > Thank You Dan,
> > I figured out my mistake. I will write you after correcting it. Thank you
> > for your help. It is really useful.
> > Just one question (for curiosity), why you have taken the last frame of
> the
> > run as the reference structure? Shall I consider the* minimal energy
> > structure*, the* last snap structure* or the *average structure* as the
> > reference structure? I have read various papers in which they have used
> > different different approaches. Which one is more accurate?
> >
>
> This depends on what exactly you're trying to look at. If you're
> interested
> to see how much a protein moves away from its starting conformation, you
> obviously use the first structure. The last structure is typically a
> reasonable choice if you're looking for a member of an equilibrated
> ensemble. The average structure is a good option if you're looking for,
> well, deviations from the average. The literature is full of examples
> where
> researchers used different references for different reasons. I suggest you
> try and place the particular researcher's choice in the context of their
> work and try to figure out why they used that particular reference for
> their
> particular application.
>
> Good luck!
> Jason
>
>
> >
> > Hirdesh
> > On Thu, Oct 7, 2010 at 4:14 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > I've done a test with VMD 1.8.7 and PTRAJ from AT 1.4.
> > >
> > > run0.pdb from run0.rst7 (last frame of run0.nc).
> > >
> > > PTRAJ:
> > > trajin run0.nc
> > > reference run0.pdb
> > > rms reference out rmsd.dat .N,CA,C time 1.0
> > >
> > > VMD:
> > > Trajectories:
> > > 0 run0.pdb
> > > 1 run0.nc
> > > RMSD Trajectory Tool:
> > > Ref: Selected (highlighted run0.pdb in trajectory list)
> > > Trajectory Frame ref: 0
> > > Selection: all (also checked backbone)
> > >
> > > The deviation between the RMSD values generated by VMD and those
> > > generated by PTRAJ is < 0.001. Are you absolutely certain you have the
> > > correct reference selected in VMD?
> > >
> > > -Dan
> > >
> > > On Wed, Oct 6, 2010 at 1:22 AM, hirdesh kumar <hirdeshs8.gmail.com>
> > wrote:
> > > > Hi Dan,
> > > > here I am proving you the detail which you were asking:
> > > >
> > > > 1) In VMD, which module did you use to calculate RMSD (RMSD Tool or
> > > > RMSD Trajectory Tool), what selection did you use, what options did
> > > > you have checked, and what structure was chosen as your reference?
> > > > I used the RMSD Trajectory tool. In that I first aligned the
> > trajectories
> > > to
> > > > the pdb generated using ambpdb after equilibration. Then I calculated
> > the
> > > > rmsd for the backbone atoms (Backbone atom definition: C CA N) And I
> > got
> > > the
> > > > rmsd in the range of 6-8.
> > > >
> > > > 2) For ptraj, send your complete ptraj.in.
> > > >
> > > > trajin prod1.crd
> > > > reference eq2.pdb
> > > > rms reference out rmsd_to_lowest_energy_struct.dat .N,CA,C time 1.0
> > > >
> > > >
> > > > Hirdesh
> > > >
> > > >>
> > > >>
> > > >>
> > > >>
> > > >
> > > >
> > > >>
> > > >> -Dan
> > > >>
> > > >> On Tue, Oct 5, 2010 at 2:25 AM, hirdesh kumar <hirdeshs8.gmail.com>
> > > wrote:
> > > >> > Hi Kshatresh,
> > > >> > Sorry for incomplete Information. In my previous mail I forgot to
> > > mention
> > > >> > that the I am getting high value in VMD and the low value is from
> > > Ptraj
> > > >> of
> > > >> > amber. I did not calculated the average structure of the entire
> run,
> > I
> > > >> just
> > > >> > calculated the pdb structure after the equilibration phase. Do I
> > need
> > > to
> > > >> > calculate the average structure of the entire run and then
> calculate
> > > the
> > > >> > rmsd w.r.t. to that structure.
> > > >> >
> > > >> >
> > > >> > Hirdesh
> > > >> >
> > > >> > On Tue, Oct 5, 2010 at 11:29 AM, Kshatresh Dutta Dubey
> > > >> > <kshatresh.gmail.com>wrote:
> > > >> >
> > > >> >> Hi Hirdesh,
> > > >> >>
> > > >> >> May i know at which simulation time have u saved your pdb? Have u
> > > >> >> calculated
> > > >> >> average structure of complete simulation?
> > > >> >>
> > > >> >> On Tue, Oct 5, 2010 at 11:21 AM, hirdesh kumar <
> > hirdeshs8.gmail.com>
> > > >> >> wrote:
> > > >> >>
> > > >> >> > Hi All,
> > > >> >> > I calculated the rmsd for my protein of interest by aligning it
> > to
> > > the
> > > >> >> pdb
> > > >> >> > generated after equilibration. The value of rmsd is very high
> > when
> > > i
> > > >> >> > calculated for backbone atoms (i.e. Calpha, N) in the range of
> > 6-8.
> > > >> The
> > > >> >> > same
> > > >> >> > calculation using amber ptraj module gave me the rmsd value of
> > > around
> > > >> one
> > > >> >> > throughout the production phase.
> > > >> >> > Now I am wondering which one should I take for my further
> > > >> consideration.
> > > >> >> >
> > > >> >> >
> > > >> >> > Hirdesh
> > > >> >> > _______________________________________________
> > > >> >> > AMBER mailing list
> > > >> >> > AMBER.ambermd.org
> > > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >> >> >
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> > > >> >>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Thu Oct 07 2010 - 07:00:03 PDT
