VMD-L Mailing List

From: Wen Li (liw_at_wadsworth.org)
Date: Fri Apr 01 2005 - 13:23:07 CST

Dear Dr. Gracia,

Thanks you very for your kind help.

I followed the procedure that you wrote. Now I am wondering what should I
fill in the "selection box" - this is an RNA molecule, and I want to
align all P atoms to the reference.

Thanks,
Wen

On Fri, 1 Apr 2005, Luis Gracia wrote:

> Hi,
>
> the rmsdtt plugin works the same way as the 'rmsd tool' plugin, except
> it loops through trajectories. For that reason a few options were added,
> plus some improvements over the 'rmsd tool' plugin. This new options are
> explained in the web;
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html
>
> For your case you can:
> - load the reference structure in another molecule and select it as the
> 'top' molecule.
> - press the 'only active' button to update the list in the rmsdtt
> plugin. The list should now include all the molecules (or trajectories)
> you want to calculate the rmsd, included the reference.
> - select the 'top' option in rmsdtt.
> - activate the 'trajectory option' in rmsdtt.
> - choose your 'plot' and 'save' options.
> - press the rmsd button to get an rmsd (optional)
> - press the align button to align.
> - press the rmsd button again to obtain the final rmsd.
>
> Hope this helps.
>
> Luis
>
> Wen Li said the following on 04/01/05 12:15:
>
> >Hello Everyone,
> >
> >I am wondering if there is a User's guide for RMSDTT in vmd - I am trying
> >to align an MD trajectory to a reference structure which is not in the
> >trajectory.
> >
> >From the window of RMSD trajectory Tool, it seems to me like that the
> >reference structure comes from a frame of the trajectory. If my reference
> >is not in the trajectory, how I can make it? My trajectory file was
> >generated from AMBER.
> >
> >I appreciate any help.
> >
> >Wen
> >
> >
>
>
> --
> Luis Gracia, PhD
> Department of Physiology & Biophysics
> Weill Medical College of Cornell University
> 1300 York Avenue, Box 75
> New York, NY 10021
>
> Tel: (212) 746-6375
> Fax: (212) 746-8690
> lug2002_at_med.cornell.edu
>
>
>