VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 26 2009 - 23:59:51 CDT

Hi,
  You should be able to do this using the RMSD Trajectory Tool or
one of the many RMSD related example scripts, by providing an appropriate
atom selection using the "within" or "exwithin" keywords as necessary.
If you need help with understanding how to use those, see the VMD User's
Guide, and/or the VMD tutorials.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

 
On Sun, Apr 12, 2009 at 06:02:13PM +0200, priyodorshi satpati wrote:
> Dear All,
>
> I am a new user of VMD. Your suggestions related to the following query will
> be of great help.
>
> A protein is trimmed to a *28* Angstrom sphere along with harmonic
> restraint applied to the outer shell (from 22 to 28 Angstom). Now I have the
> NAMD traj file of this protein alongwith overlayed water sphere. From the
> traj file i want to calculate the RMS deviation for the protein atoms *only
> within 22 Angstrom radius*. How to modify the *rmsd.tcl* file of VMD to do
> this.
>
> thank you very much...
>
>
> Regards
>
> Priyadarshi
>
> --
> Dr. Priyadarshi Satpati
> Biocomputing and Structure research Group,
> Laboratoire de Biochimie,
> Ecole Polytechnique,
> 91128 Palaiseau, France
>
> Phone (Res) : +33/(0)1 69 33 27 66
> (Off) : +33/(0)1 69 33 48 94
> (Mob) : +33/(0)6 27 75 56 49 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078