VMD-L Mailing List

From: Jindal Shah (jindal.shah_at_gmail.com)
Date: Wed Aug 24 2005 - 11:35:11 CDT

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
>
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> NIH Resource for Macromolecular Modeling and Bioinformatics
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>