VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 12 2010 - 15:25:35 CDT

Hirdesh,
  I'm sure that the issue here is that your two alignments aren't being
done exatly the same way in both packages, or that the atoms you're
selecting aren't the same...

You will need to provide much more detail in order for others to help you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 05, 2010 at 11:20:32AM +0530, hirdesh kumar 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 condiration.
> any help will be appreciated.
> Thanks
>
> Hirdesh 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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