VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 16 2010 - 21:50:07 CDT

Try un-checking "backbone only" and see if that cures your problem.
With CG structures, atom names may not match those of standard PDB
structures, which are more what VMD is expecting when selections like
"backbone" etc are used.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 16, 2010 at 09:29:13PM -0400, Gregorio Alanislobato wrote:
> Hi everyone,
>
> I've got two coarse grained proteins with 130 atoms each and no matter
> what selection I type in the RMSD calculator, I obtain the message
> "Selection contains no atoms. RMSD calculation not possible". What can be
> wrong?
>
> Thanks again.
>
> Regards,
> --
> Gregorio Alanis Lobato, BSc
> 4700 KAUST Mail Box: 1899
> Thuwal 23955*6900, KSA
> Student ID: 100037943
> Badge #: 101969
> Mobile Phone: +966-564-75-14-14
> e-mail: gregorio.alanislobato_at_kaust.edu.sa
>
> On 16 August 2010 14:58, Mert Gu:r <gurmert_at_gmail.com> wrote:
>
> Dear Gregorio,
> Type "name CA" instead of "protein" in the RMSD plugin
> Best,
> Mert
> On Mon, Aug 16, 2010 at 8:13 PM, Gregorio Alanislobato
> <gregorio.alanislobato_at_kaust.edu.sa> wrote:
> > Hi,
> >
> > I would like to measure the RSMD between two coarse grained molecules
> but
> > VMD keeps saying it is not possible. Do anyone know of a way to do
> this?
> >
> > Thanks in advance.
> >
> > Regards,
> > --
> > Gregorio Alanis Lobato, BSc
> > 4700 KAUST Mail Box: 1899
> > Thuwal 23955*6900, KSA
> > Student ID: 100037943
> > Badge #: 101969
> > Mobile Phone: +966-564-75-14-14
> > e-mail: gregorio.alanislobato_at_kaust.edu.sa
> > 

-- 
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