Re: AMBER: "matrix" in ptraj

From: Holger Gohlke <>
Date: Sat, 24 Apr 2004 13:47:41 +0200

Sichun Yang schrieb:
> Dear all,
> I am trying to corvariance matrix by ptraj.
> The action "rms" is fine.
> But when I used "matrix", there is no output at all.
> Any suggestion is welcome.
> Here is my input:
> reference native.prmcrd
> trajin all.dcd

Using the ptraj commands below on one of my trajectory files, I get an
output to "distmat.dat". What is written in the ACTIONS section of the
ptraj output in your case? I get:

  1> RMS to reference structure (1rrb_vac.inpcrd) using mass weighting
      Atom selection follows :2-75.N,CA,C
  7> CENTER to origin via center of mass, atom selection follows :2-75
  7> IMAGE by molecule to origin using the center of mass, atom
selection * (All atoms are selected)
  7> MATRIX: Calculating covar matrix by atom, dumping to file
distmat.dat, using no mass weighting
      Atom selection 1 follows :1-76.CA

If you don't find any error, you might want to send me a (short) piece
of your trajectory file along with the prmtop file.

Best regards


> rms reference mass :2-117.CA,C,N
> center :2-117 mass origin
> image origin center
> matrix covar .CA out distmat.dat
> have a nice weekend.
> Best,
> Sichun
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!!!      Please note new telephone number      !!!
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
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Received on Sat Apr 24 2004 - 12:53:01 PDT
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