Prasad Gajula wrote:
Dear Dr. David,
Thank you very for the reply.
When i looked the energy minimized average structure it looks just fine.
??
but you did not say energy minimized... check the rmsd between average
and minimized average structure as well.
Maybe you want to do a clustering analysis instead?
I calcualted the average structure from the simulation trajectory. when
I
calculate the rmsd of the protein to this average sturture, it is giving
average rmsd of 0.16 nm. But, it is not clear for me why the average
sturcture is never adapted rmsd near (or equal) to zero. I did not
calculate the rmsd with respect to the starting structure either.
Any clue?
the average structure is unphysical, it may have long bonds etc.
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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