VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Wed Jul 28 2010 - 07:55:33 CDT

Dear Leo

Thanks.

This is the command i'm using

"rmsd_matrix -mol top -seltext name CA -frames all -fit none -o 2d_plot.txt"
usage: rmsd_matrix ?-arg var?...
  -mol <molid> (default: top)
  -seltext <selection text> (default: backbone)
  -frames <begin:end> or <begin:step:end> or all or now (default: all)
  -fit <selection text> (default: backbone)
  -o <filename>
error: empty argument list or odd number of arguments -mol top -seltext name
CA -frames all -fit none -o 2d_plot.txt

Many Thanks
Balaji

On Wed, Jul 28, 2010 at 1:50 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:

> On Wed, Jul 28, 2010 at 2:45 PM, ban arn <ban.arn_at_gmail.com> wrote:
> > Dear Leonard
> >
> > Thanks for the reply.
> >
> > I have saved trajectories containing only CA atoms.
> >
> > And in the command, i'm mentioning c-alpha atoms as "name CA in seltext",
> > but it shows error as atomselect: cannot parse selection text: CA.
> >
> > Could you please tell me how to specify c-alpha atoms so that VMD can
> read
> > it.
>
> Didn't I answer your question yesterday? What exactly is the command
> that you are using (please copy and paste it)?
>
> Leo
>
> > Many Thanks
> > Balaji
> >
> > On Wed, Jul 28, 2010 at 12:24 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu
> >
> > wrote:
> >>
> >> Dear Balaji,
> >>
> >> On Wed, Jul 28, 2010 at 12:50 PM, ban arn <ban.arn_at_gmail.com> wrote:
> >> > Dear All
> >> >
> >> > I would like to plot 2D rmsd matrix for C-alpha atoms through my
> >> > trajectories.
> >> >
> >> > Is any script available for this in VMD
> >>
> >> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/rmsd_matrix/
> >>
> >> Cheers,
> >> Leo
> >>
> >> > Kindly advice.
> >> >
> >> > Many Thanks
> >> > Balaji
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Leonardo Trabuco, Ph.D.
> >> CellNetworks, BioQuant
> >> University of Heidelberg, Germany
> >
> >
>
>
>
> --
> Leonardo Trabuco, Ph.D.
> CellNetworks, BioQuant
> University of Heidelberg, Germany
>