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
> >> > _______________________________________________
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> >> >
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>
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Received on Tue Oct 05 2010 - 22:30:02 PDT
