VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 19 2007 - 14:02:49 CST

Hi,
  If you load a PSF for your structure, then VMD will use that
information verbatim without any re-interpretation. If you have already
loaded a PDB or other files that contain partial or complete bond information
followed by a PSF, the PSF will replace any previous bond information.
It sounds to me like your original PSF lacks these bonds.
The only other possibility that I can think of is that you might be using
an old version of VMD or a beta version that might have a bug that's
subsequently been fixed. Since you didn't mention what version of VMD
you're using, I'll have to assume that the problem is with your PSF file.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 14, 2007 at 06:52:24AM -0800, Dongsheng Zhang wrote:
> Hello, VMD users,
>
> I have a polymer gel. When I tried to display it, I found some bonds between monomers are missing, even though I had given a psf file. I am wondering if VMd makes its own choice of bonding or following the bonding information in psf file.
>
> VMD always looks for data in its default directory. Is it possible to change the default directory?
>
> P.S. My VMD is windows version.
>
> Have a nice day!
>
> Dongsheng
>
>
>
>
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-- 
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