AMBER Archive (2008)

Subject: AMBER: PCA analysis

From: Ibrahim Moustafa (
Date: Mon Jun 02 2008 - 16:09:17 CDT

Dear all,

  I have posted a question yesterday about the PCA analysis and was hoping
to get some help from PTRAJ developers and expert users.
Iım posting the question again. I googled through the archive but could not
find an answer. It is noticeable that related questions posted by others got
no answer too!
Is there something special or is it just a coincidence? The manual of PTRAJ
gives a brief description of its tools. So, I wish to hear from people did
similar analysis in PTRAJ.

 Here is my question ( I tried to make it shorter for busy people)
    Iım trying to do PCA on a 20 ns trajectory and Iım new to this type of
analysis. The script used to do the analysis and parts of the outputs are
given at the end.
Iım analyzing the first 10 PCs and want to look at the PCs individually so I
can visualize the corresponding displacements on the structure.
The rmsd value corresponding to the st1 PC is very low, which I donıt
understand as the 1st eigenvector accounts for about 32 % of the total
Iım not doing Normal Mode to expect the 1st 6 PC close to zero. However,
this is the case with the PCA analysis I did. So what am I missing here??
I expected to have the largest fluctuations for the highest eigenvalue
(PC1)...which is not the case here. What does analyze mode exactly do?

Example of the command used:

Tarjin trejectoryfile.mdcrd
Rms first @CA
Matrix covar name pcacovar @CA out pcacovar.mat
Analyze matrix pcacovar out eigenvec.dat name eigenvect vecs 50
Analyze modes fluct stack eigenvect out rmsfluct_PC1.dat beg 1 end 1
Analyze modes fluct stack eigenvect out rmsfluct_PC2.dat beg 2 end 2

Example of output:
#Eigenvector matrix output
1 218.63728
-0.00750 -0.01603 -0.00507 -0.00535 -0.01348 -0.00057 -0.00379
   -0.01278 0.00106 -0.00213 -0.02327 0.00619 0.00277
    0.01126 0.00597 -0.02036 0.00711 0.00763 -0.02560

# The rmsd analysis of the 1st PC looks like that:
Analysis of modes: RMS FLUCTUATIONS
  Atom no. rmsX rmsY rmsZ rms
         1 0.003 0.006 0.002 0.007
         2 0.002 0.005 0.000 0.006
         3 0.001 0.005 0.000 0.005

#The rmsd analysis of 10th PC
 Analysis of modes: RMS FLUCTUATIONS
  Atom no. rmsX rmsY rmsZ rms
         1 0.078 0.188 0.038 0.207
         2 0.132 0.170 0.109 0.242
         3 0.004 0.071 0.019 0.074

  Thanks in advance for your help,


Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802

Tel. (814) 863-8703 Fax (814) 865-7927

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