VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 15 2005 - 14:05:54 CDT

Bob,
  Can you send me the structure that gives you trouble?
I'll take a look at it. Most likely VMD thinks that there's a bond
between different types of residues (VMD's internal classifications)
that it's not happy about. If you send me the files, I'll load it up
and get back to you in a few days when I've had a chance to investigate
a bit. I'm already looking at some other structures people have sent
me so I won't be able to get to it for a little while.

  John

On Mon, Aug 15, 2005 at 02:54:28PM -0400, Bob Johnson wrote:
> Hello everyone,
> I am generating a single strand of DNA with Amber's Nucgen. However, when I
> visualize it with VMD I get a message saying that there is an unusual bond
> between residues 1 and 2 of the DNA strand. This message doesn't prevent VMD
> from drawing the molecule. I measured the bond length and it seems fine. There
> is not noticeable reason why VMD is giving this message. I wouldn't care except
> that, because of this message, VMD doesn't draw the molecule correctly using the
> Ribbons visualization. It leaves off the last base: the one VMD complains about.
> Does anyone know how to fix this?
> Thanks,
> Bob Johnson 

-- 
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