VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 19 2006 - 11:50:07 CDT

Hi,
  You mentioned that you encountered a "bug" in some tool, can you be
more specific as to what bug you encountered and what tool you were using?
Was it a tool in the VMD extensions menu, or a script someone made available,
or something else?

In any case, you can calculate the per-atom RMSF values using the
'measure rmsf' command in VMD. If you want RMSD, then use the 'measure rmsd'.

You asked about plotting versus timestep rather than versus frame.
VMD only does these calculations versus frames, so if you want to change
the temporal coordinate from frame to timestep, you need to know what
the delta T per frame is in the trajectory you've loaded.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 18, 2006 at 04:42:53PM +0530, genie lfs wrote:
> hello all
>
> i am trying to study rna-protein interactions.
>
>
> i would like to know how to find rmsf of single residues ? the residue
> rmsd seems to have a bug and points to rms calculator?
>
> and is there any way i can plot rmsd changes along time steps instead
> of frames ( tried it but did not get it).
>
> and i want to know the role played by enviornment(water and ions). is
> there any tool which can give me the effect of enviornment on the
> interactions between rna and protein?
>
> thanking you.
> santhu 

-- 
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