VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 12 2009 - 09:58:01 CDT

Hi,
  If your PDB file contains "CONECT" records, VMD may load these.
You can prevent VMD from using automatic bonds or CONECT records by
loading the file like this:
  mol new foo.pdb filebonds off autobonds off
or
  mol addfile foo.pdb filebonds off autobonds off

Cheers,
  John Stone
  vmd_at_ks.uic.edu

On Wed, Aug 12, 2009 at 09:27:55AM -0400, Liang, Linus H. wrote:
> Dear all,
>
> I'm working with a carbon nanopore structure and I'm trying to remove all the bonds between the carbons. However, when I uploaded a new psf file with 0 bonds angles and dihedrals, VMD automatically bonds the carbon atoms back together when I load up the pdb file.
>
> Thanks for your help in advance,
>
> Linus
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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