AMBER Archive (2009)

Subject: [AMBER] How to use AMBER 10 for PCA analysis.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Sep 01 2009 - 10:30:56 CDT

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?

 

Bset 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

...........

--------------------------------------------------------------------------

 

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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