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.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.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
>
> Holger
>
> > 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
> Germany
>
> Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826
> Email: gohlke.bioinformatik.uni-frankfurt.de
> URL: http://www.rz.uni-frankfurt.de/~hgohlke
> ++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Sun Apr 25 2004 - 00:53:00 PDT
