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 - 23:00:04 PDT
