VMD-L Mailing List

From: Dongsheng Zhang (dong_at_pampas.chem.purdue.edu)
Date: Mon Jun 19 2006 - 13:17:23 CDT

Dear Jeff,

Thank you very much for your reply. I made a careless mistake. I have
changed atom names unconsciously by using my old awk script.

Have a nice day!

Dongsheng

On Mon, 2006-06-19 at 12:20 -0400, Jeffrey A Tibbitt wrote:
> I know VMD draws bonds based on distances, but you haven't changed the
> distances. A good thing to do regardless of this problem is to generate a
> psf for your original pdb file(s). Then after you load in your new pdb
> file, load in the psf for that structure. The bonds stated in the psf
> override the distance bonds of VMD. However, to do this, you'll need a
> topology file containing the bond information for that molecule. Other
> than that, you can add in CONNECT lines to your pdb file to define the
> bonds. I think VMD can interpret that data to draw the correct bonds.
> That's all I can think of now.
>
> Jeff
>