AMBER Archive (2009)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Jul 30 2009 - 05:37:49 CDT

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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