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From: Thomas E. Cheatham, III <cheatham.chpc.utah.edu>

Date: Wed, 19 Jan 2005 11:16:17 -0700 (Mountain Standard Time)

I am forwarding this to the AMBER e-mail list where more qualified people

are capable of answering your question...

--tom

Date: Tue, 18 Jan 2005 16:56:10 +0330

From: amininasab <amininasab.ibb.ut.ac.ir>

Subject: ptraj analysis

I have some problem in ED analysis of my trajectory in ptraj.

I used the following trajin script:

trajin mdcrd

rms first .CA

matrix dist name distance .CA out dist-matrix

matrix covar name covariance .CA out covar-matrix

matrix correl name correlation .CA out correl-matrix

analyze matrix covariance out evectors name evecs vecs 255

analyze modes fluct out rmsfluctuation-1 stack evecs beg 1 end 1

analyze modes fluct out rmsfluctuation-2 stack evecs beg 2 end 2

analyze modes fluct out rmsfluctuation-3 stack evecs beg 3 end 3

analyze modes fluct out rmsfluctuation-4 stack evecs beg 4 end 4

analyze modes fluct out rmsfluctuation-5 stack evecs beg 5 end 5

analyze modes fluct out rmsfluctuation-6 stack evecs beg 6 end 6

analyze modes fluct out rmsfluctuation-7 stack evecs beg 7 end 7

analyze modes fluct out rmsfluctuation-8 stack evecs beg 8 end 8

analyze modes fluct out rmsfluctuation-9 stack evecs beg 9 end 9

analyze modes fluct out rmsfluctuation-10 stack evecs beg 10 end 10

analyze modes fluct out rmsfluctuations stack evecs beg 1 end 10

analyze modes displ out rmsdisplacement-1 stack evecs beg 1 end 1

analyze modes displ out rmsdisplacement-2 stack evecs beg 2 end 2

analyze modes displ out rmsdisplacement-3 stack evecs beg 3 end 3

analyze modes displ out rmsdisplacement-4 stack evecs beg 4 end 4

analyze modes displ out rmsdisplacement-5 stack evecs beg 5 end 5

analyze modes displ out rmsdisplacement-6 stack evecs beg 6 end 6

analyze modes displ out rmsdisplacement-7 stack evecs beg 7 end 7

analyze modes displ out rmsdisplacement-8 stack evecs beg 8 end 8

analyze modes displ out rmsdisplacement-9 stack evecs beg 9 end 9

analyze modes displ out rmsdisplacement-10 stack evecs beg 10 end 10

analyze modes displ out rmsdisplacements stack evecs beg 1 end 10

go

The first problem is about the number of eigenvectors and eigenvalues.

My protein has 85 amino acids and using CA should produce 255

eigenvectors and eigenvalues but in my output file (evectors) there are

only 254 items and one of them is missing. The last five eigenvalues are

zero and it seems the reminding zero eigenvalue is not reported. The

similar situation reported by my freinds.

The next problem are about "analyze modes fluct" and "anayze modes

displ", Would you please tell me the physical or geometrical meaning of

those commands and why the RMS of CA's for the bigger eigenvalues are

smaller.

For clarity I attached some output files.

Looking forward you and thanks in advance.

sincerely yours,

Mehriar Amininasab,PhD

Inst. of Biochem. & Biophys.,

P.O. Box 13145-1384,

Univ. of Tehran,

Tehran-IRAN

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Received on Wed Jan 19 2005 - 18:53:01 PST

Date: Wed, 19 Jan 2005 11:16:17 -0700 (Mountain Standard Time)

I am forwarding this to the AMBER e-mail list where more qualified people

are capable of answering your question...

--tom

Date: Tue, 18 Jan 2005 16:56:10 +0330

From: amininasab <amininasab.ibb.ut.ac.ir>

Subject: ptraj analysis

I have some problem in ED analysis of my trajectory in ptraj.

I used the following trajin script:

trajin mdcrd

rms first .CA

matrix dist name distance .CA out dist-matrix

matrix covar name covariance .CA out covar-matrix

matrix correl name correlation .CA out correl-matrix

analyze matrix covariance out evectors name evecs vecs 255

analyze modes fluct out rmsfluctuation-1 stack evecs beg 1 end 1

analyze modes fluct out rmsfluctuation-2 stack evecs beg 2 end 2

analyze modes fluct out rmsfluctuation-3 stack evecs beg 3 end 3

analyze modes fluct out rmsfluctuation-4 stack evecs beg 4 end 4

analyze modes fluct out rmsfluctuation-5 stack evecs beg 5 end 5

analyze modes fluct out rmsfluctuation-6 stack evecs beg 6 end 6

analyze modes fluct out rmsfluctuation-7 stack evecs beg 7 end 7

analyze modes fluct out rmsfluctuation-8 stack evecs beg 8 end 8

analyze modes fluct out rmsfluctuation-9 stack evecs beg 9 end 9

analyze modes fluct out rmsfluctuation-10 stack evecs beg 10 end 10

analyze modes fluct out rmsfluctuations stack evecs beg 1 end 10

analyze modes displ out rmsdisplacement-1 stack evecs beg 1 end 1

analyze modes displ out rmsdisplacement-2 stack evecs beg 2 end 2

analyze modes displ out rmsdisplacement-3 stack evecs beg 3 end 3

analyze modes displ out rmsdisplacement-4 stack evecs beg 4 end 4

analyze modes displ out rmsdisplacement-5 stack evecs beg 5 end 5

analyze modes displ out rmsdisplacement-6 stack evecs beg 6 end 6

analyze modes displ out rmsdisplacement-7 stack evecs beg 7 end 7

analyze modes displ out rmsdisplacement-8 stack evecs beg 8 end 8

analyze modes displ out rmsdisplacement-9 stack evecs beg 9 end 9

analyze modes displ out rmsdisplacement-10 stack evecs beg 10 end 10

analyze modes displ out rmsdisplacements stack evecs beg 1 end 10

go

The first problem is about the number of eigenvectors and eigenvalues.

My protein has 85 amino acids and using CA should produce 255

eigenvectors and eigenvalues but in my output file (evectors) there are

only 254 items and one of them is missing. The last five eigenvalues are

zero and it seems the reminding zero eigenvalue is not reported. The

similar situation reported by my freinds.

The next problem are about "analyze modes fluct" and "anayze modes

displ", Would you please tell me the physical or geometrical meaning of

those commands and why the RMS of CA's for the bigger eigenvalues are

smaller.

For clarity I attached some output files.

Looking forward you and thanks in advance.

sincerely yours,

Mehriar Amininasab,PhD

Inst. of Biochem. & Biophys.,

P.O. Box 13145-1384,

Univ. of Tehran,

Tehran-IRAN

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

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- APPLICATION/OCTET-STREAM attachment: evectors

- APPLICATION/OCTET-STREAM attachment: rmsfluctuation-1

- APPLICATION/OCTET-STREAM attachment: rmsfluctuation-2

- APPLICATION/OCTET-STREAM attachment: rmsfluctuation-3

- APPLICATION/OCTET-STREAM attachment: rmsfluctuation-4

- APPLICATION/OCTET-STREAM attachment: rmsfluctuation-5

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