[AMBER] PCA analysis: the first vector is the movement of whole molecule.

From: Catein Catherine <askamber23.hotmail.com>
Date: Thu, 30 Jul 2009 11:37:49 +0100

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,



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
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