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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Received on Mon Oct 04 2010 - 23:30:05 PDT
