VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 15 2005 - 14:05:54 CDT
- Next message: John Stone: "Re: Visualizing an infinite carbon nanotube"
- Previous message: Bob Johnson: "Problem with DNA bonds"
- In reply to: Bob Johnson: "Problem with DNA bonds"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: John Stone: "Re: Visualizing an infinite carbon nanotube"
- Previous message: Bob Johnson: "Problem with DNA bonds"
- In reply to: Bob Johnson: "Problem with DNA bonds"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]