AMBER Archive (2004)

Subject: Re: AMBER: "matrix" in ptraj

From: Sichun Yang (syang_at_physics.ucsd.edu)
Date: Sat Apr 24 2004 - 18:20:50 CDT

Thank you for your response.

Here is my output for my trajectory files.
It seems the action 'matrix' is skipped for some reason.
by the way, I am using AMBER7, but I updated ptraj by ptraj-6.5.tar.Z.

ACTIONS
  1> RMS to reference structure (native.prmcrd) using mass weighting
      Atom selection follows :2-117_at_N,CA,C
  7> CENTER to origin via center of mass, atom selection follows :2-117
  7> IMAGE by molecule to origin using the center of mass, atom
selection *
(All atoms are selected)
 
 
Processing AMBER trajectory file md.crd

Set 1 .................................................
Set 50 .................................................

Best,
Sichun

On Sat, 24 Apr 2004, Holger Gohlke wrote:

> 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:
>
> ACTIONS
> 1> RMS to reference structure (1rrb_vac.inpcrd) using mass weighting
> Atom selection follows :2-75_at_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_at_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
>
> Holger
>
> > rms reference mass :2-117_at_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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> --
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> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
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>
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> Fachbereich Biologie und Informatik
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>
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