VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Wed Jul 28 2010 - 07:45:52 CDT

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.

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
>