AMBER Archive (2009)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Jul 30 2009 - 22:46:49 CDT

Dear Sir/Madam,

 

This is the reasons why I ask, I expect the rotation and translation motion of whole molecule should be removed from PCA analysis, by using "rms first *". The rotation and translation motion of whole molecule could not be the purpose of doing PCA. Why does it related to the length of the simulation?

 

As suggested by IED webpage, "rms first *" was used, What is the meaning of *?

 

Best regards,

Cat
 
> Subject: Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule.
> From: hannes.loeffler_at_stfc.ac.uk
> To: amber_at_ambermd.org
> Date: Thu, 30 Jul 2009 11:52:48 +0100
>
> On Thu, 2009-07-30 at 18:37 +0800, Catein Catherine wrote:
> > 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?
>
>
> Are you suggesting to ignore a results because it doesn't meet your
> expectations? Are you confident that you have simulated long enough?
>
>
> > I have used rms first * in the ptraj run already. Did I miss any
> > important things or the result is just normal?
>
> The point of initial fitting is to remove rotations and translations.
> What does the mask "*" refer to?
>
>
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