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
> > >> >> >
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 07 2010 - 06:30:02 PDT
