VMD-L Mailing List

From: hirdesh kumar (hirdeshs8_at_gmail.com)
Date: Tue Oct 05 2010 - 00:50:32 CDT

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