VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 23 2011 - 09:06:23 CDT

How is your file named, and how did you load it? The Gromos/Gromacs plugin
in VMD knows how to read a few different file formats, and it
knows some are in nanometers and that they need to be automatically
converted. Perhaps you're loading the file in such a way that the
plugin doesn't recognize this and/or just isn't doing the conversion...

Cheers,
  John

On Tue, Aug 23, 2011 at 06:49:22AM -0400, Moeed wrote:
> Hi John,
>
> Thanks. Yes, I am using gro. file which uses nanometers. This means every
> time I have to change the units?
>
> On Mon, Aug 15, 2011 at 12:21 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> This is usually caused by problems with the interpretation of the
> coordinate units in the files being loaded. Is it possible that you've
> got your atomic coordinates in units of nanometers, but have saved them
> to a file format (e.g. PDB) that expects Angstroms?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Mon, Aug 15, 2011 at 12:09:51PM -0400, Moeed wrote:
> > Hello all,
> >
> > I have a problem visualizing my structure in vmd. Once I load
> structure
> > and trajectory files file I see some artificial bonds connecting
> all atoms
> > while there is no bond between them. Has anyone any ideas why this
> is
> > happening?
> >
> > Thank you,
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

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