VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 18:11:57 CDT

Jindal,
  If you want me to have a look at your PDB, send me a copy of it and I'll
test it with the newest version of VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 24, 2005 at 12:35:11PM -0400, Jindal Shah wrote:
> Thank you for the input. I did check my PDB file and the units are in
> Angstroms. VMD consoles shows large number of errors and then displays the
> molecules..
>
> Jindal
>
> On 8/24/05, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > Have you checked to make sure you have the right units in your
> > PDB/XYZ file? VMD assumes the units are in Angstroms. That would
> > easily cause problems with bond determination. When using autobonds 0
> > you'll want to display the molecule using VDW or one of the other space
> > filling reps since the atoms will otherwise be drawn as tiny points when
> > you use the default "lines" mode since there aren't any bonds to draw.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Aug 24, 2005 at 11:06:09AM -0400, Jindal Shah wrote:
> > > Hello,
> > > I am trying to view trajectory of water molecules in VMD. When I load a
> > pdb
> > > or xyz file, the bonds are automatically generated which returns errors
> > due
> > > to maximum number of bonds exceeded. I checked the vmd mailing list and
> > > found that the following solution was suggested
> > >
> > > mol new myfile.pdb autobonds 0
> > >
> > > However, it does not work for me? My pdb or xyz file does not contain
> > any
> > > information.
> > >
> > > Any suggestions?
> > > Thank you.
> > >
> > > Jindal
> >
> > --
> > 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
> > 

-- 
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