From: John Stone (
Date: Mon Mar 08 2004 - 17:28:46 CST

  If you want more details about what's going on with your system, it
would be very helpful if you actually gave me the exact error messages
VMD is printing, along with the structure file that causes you problems.
I assume that you're loading a file type that doesn't include bond information?
Its quite possible that you're having problems due to closely packed
atoms combined with the use of a file format that doesn't provide bonding
information, in which case VMD is forced to guess and occasionally has
difficulties as you describe. You didn't mention whether you compared the
location of residue XXX with the location of YYY are they in fact neighbors?


On Sat, Mar 06, 2004 at 05:31:27AM -0500, Satyavani Vemparala wrote:
> Hello:
> when i try to load a molecule, i get the error :
> unusual bond between residues XXX and YYY.
> but when i actually look at residue XXX, and try to see anything within
> 2-3 A distance, i find nothing.. so i don't understand this error.
> also is there a way to locate these warning atoms in VMD, just the bad
> guys. Also i get an wrror of residue exceeded maximum number of bonds..
> but doesn't specify particularly which residue and all other relevant
> info.
> Thanks
> VAni
> --

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:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078