Dear Sir/madam,
I have did a PCA analysis, the first vector did not involve movement of a sub-domain of the protein, but the rotate/movement of the whole protein. While the 2nd and forward vector involve the movement of sub-domain. Is it normal results to find the whole molecule movement as the first PCA vector? Should I neglect the first PCA result in this case?
I have used rms first * in the ptraj run already. Did I miss any important things or the result is just normal?
Best regards,
Cat
PS.Thank you very much to the amber experts in the forum. I can view my PCA data now. Many thanks again!
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Received on Wed Aug 19 2009 - 19:48:07 PDT
