VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon Aug 21 2000 - 13:32:52 CDT

Hi Lars,

I've never used MacroModel, but one reason VMD might be getting confused is
if MacroModel were using different atom names for the DNA backbone than what
VMD expects. I haven't worked much with DNA models, but here are some comments
from the part of the code that parses the structure:

  // search for the DNA/RNA backbone; the atom names are:
  // for the phosphate: P, O1P, O2P
  // for the rest: O3', C3', C4', C5', O5'
  // (or O3*, C3*, C4*, C5*, O5*)

If you're not using these names, converting them might cure VMD's confusion.

Hope this helps,

Justin

>
> Hi,
> i have a DNA-double strand which was modelled with MacroModel. When i
> try to draw the backbone as tube, trace or ribbon, i get only
> fragments of the 'tube' and not the two backbones.
> During loading of the structure, i get error-messages like:
> Unusual bond between residue X and Y
>
> Fragments: 4 ... Nucleic:8 (nontheless that i have only a
> DNA-doublestrand)
>
> What is the problem and how can i fix it (with Windows NT or Irix
> 6.5)
>
> thanks
>
> Lars
> _________________________________
> Lars Burgdorf
> Philipps-Universität Marburg
> FB Chemie
> AG Carell
> 35032 Marburg
>
> Tel.: +49-(0)6421-28-26 971
> Fax.: +49-(0)6421-28-22 189
> burgdorf_at_mailer.uni-marburg.de
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D