AMBER Archive (2005)

Subject: AMBER: ptraj analysis

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Jan 19 2005 - 12:16:17 CST

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_at_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                        
      

  • APPLICATION/OCTET-STREAM attachment: evectors





-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu