AMBER Archive (2009)

Subject: RE: [AMBER] Question regarding PCA analysis.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Sep 03 2009 - 21:55:42 CDT

Dear Chiris,

 

Thanks for your reply. I have been waiting for help on this topic. Yes, I should read more literature or book on PCA.

 

I got the results according to your commands. Thank you very much.

 

Best regards,

 

Cat

 

 

 

 

 

 

 

 

 

 

 

 
> Date: Thu, 3 Sep 2009 09:17:42 -0500
> Subject: Re: [AMBER] Question regarding PCA analysis.
> From: chris.moth_at_Vanderbilt.Edu
> To: amber_at_ambermd.org
>
>
>
> >
> > Dear Sir/Madam,
> >
> > After running PCA, I got two files (xxx.pev and xxx.ppj). I could like to
> > ask if I want to calculate % of total protein motions described by the
> > first eigenvector, what should I do? What is the meaning of the numbers
> > in these two files?
> >
> >
> > With reference to previous answers of the related question, I know in the
> > xxx.pev file:
> >
> >
> >
> > the first line" Eigenvectorfile: COVAR" is the tilte
> >
> > the second line "1695 = number of atoms * 3"
> >
> >
> >
> > However, I still cannot figure out what is 73.10704 42.51491.....0.0009,
> > they are not in the decending order.
>
> Apology if my response here is over-elementary, but I sense you are
> needing to get oriented in the output as first order of business.
>
> The first numbers you are seeing are the coordinates of the atoms in the
> systemat their mean positions from the ptraj run. As long as you removed
> translation and rotation correctly before creating your covariance
> matrix,these coordinates would correspond to the coordinates of the system
> at a local mimum around which a typically more challenging Normal Mode
> calculation (diagonalization of Hessian matrix) were being performed.
>
> You will find the eigenvalues and eigenvectors after these coordinates.
>
> grep --after=10 --before=1 "\*\*" ptraj.output.file | less
>
> could yield something like this. You see the the last of the coordinates.
> Then a "1" indicates the "first" Eigenvector and a 0.56814 for the
> Eigenvalue.
>
> Note that the units of the Eigenvalues varies depending on whether you do
> Mass-weighted output or not. The units are discussed elsewhere in
> documentation or on the reflector.
>
> Numbers after that are the first eigenvector, the harmonic approximations
> of the amplitude of the motion of the atom coordinates x,y,z; x,y,z; etc.
>
> Hope the above helps more than it hurts.
>
>
>
> 27.16307 37.16769 52.95533 27.24810 37.52958 53.27943 27.16547
> ****
> 1 0.56814
> 0.00180 0.00127 0.00087 0.00207 0.00124 0.00050 0.00188
> 0.00137 0.00086 0.00174 0.00134 0.00046 0.00140 0.00107
> 0.00200 0.00198 0.0
>
>
>
>
>
>
>
> What is the first eigenvector and
> > eigenvalue in this analysis? I want to calculate the % of motion
> > described by the first eigenvector, does it equal to [73.10704 / sum
> > (73.10704......0.0009)]*100%
> >
> >
> >
> > Then, what is the mean of the values in xxx.ppj files?
> >
> >
> > Best regards & many thanks,
> >
> > Cat
> >
> >
> >
> >
> > The xxx.pev files starts with
> >
> > ---------------------------------------------------------------------------
> >
> >
> >
> >
> >
> >
> >
> >
> > Eigenvector
> > file:
> > COVAR
> >
> >
> >
> >
> >
> > 1695
> > 1695
> >
> >
> >
> >
> >
> >
> > 73.10704
> > 42.51491
> > 65.46974
> > 73.51263
> > 45.08371
> > 64.03552
> > 75.46584
> >
> > 44.06115
> > 61.03077
> > 76.46655
> > 46.93481
> > 58.74557
> > 76.09958
> > 45.09636
> >
> >
> >
> >
> >
> >
> >
> > 55.40839
> > 76.08002
> > 48.42934
> > 53.48851
> > 79.68982
> > 49.11898
> > 54.59358
> >
> > 81.03393
> > 45.72585
> > 53.53507
> > 82.31487
> > 44.6972
> > 50.12527
> > 79.7907.....................................................................................0.0009
> > --------------------------------------------------------------------------
> >
> > The xxx.ppj files starts with
> >
> > -----------------------------------------------------------------------------------
> >
> >
> >
> >
> >
> >
> >
> >
> > Projection
> > of
> > snapshots
> > onto
> > modes
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Snapshot
> > Mode1
> > Mode2
> > Mode3
> > Mode4
> > Mode5
> > Mode6
> > Mode7
> > Mode8
> > Mode9
> > Mode10
> >
> >
> > 1
> > -26.927
> > 24.853
> > 5.978
> > -0.671
> > -3.39
> > 16.009
> > 2.134
> > 1.791
> > -6.824
> > 0.177
> >
> >
> > 2
> > -27.408
> > 24.742
> > 3.341
> > -0.199
> > -4.45
> > 17.883
> > 0.757
> > 3.522
> > -7.053
> > -1.57
> >
> >
> > 3
> > -27.11
> > 26.452
> > 3.71
> > 0.511
> > -3.956
> > 17.529
> > 0.793
> > 1.711
> > -6.518
> > -0.177
> >
> >
> > 4
> > -27.994
> > 25.609
> > 4.671
> > 0.121
> > -3.586
> > 16.577
> > 0.261
> > 2.362
> > -5.53
> > 0.835
> >
> >
> > 5
> > -26.922
> > 26.545
> > 6.5
> > -0.496
> > -4.567
> > 16.954
> > 2.366
> > 2.107
> > -4.384
> > 1.03
> >
> >
> > 6
> > -28.509
> > 24.969
> > 8.291
> > 0.139
> > -3.417
> > 16.243
> > 1.178
> > 2.262
> > -4.706
> > 0.511
> >
> >
> > --------------------------------------------------------------------------------------------------------------------
> >
> >
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>
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