VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 21 2009 - 23:44:35 CDT

Hi,
  For performance and memory consumption reasons, VMD uses a
fixed-sized bond list for each atom. The standard VMD builds
limit the maximum number of bonds for a single atom to 12.
If you have a genuine need to define more than 12 bonds for a
single atom, VMD can be built to allow a larger maximum
value, by editing the definition of the MAXATOMBONDS macro
at the top of Atom.h and recompiling the source code.

What kind of structure are you working with such that you need
so many bonds?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 21, 2009 at 09:01:35PM -0700, BIN ZHANG wrote:
> Dear All:
>
> While I was using the "setbonds" command in VMD, I got the following
> error:
>
> atomsel: setbonds: too many bonds in bondlist: 402 404 406 468 284 418
> 414 416 227 420 470 411 409
> Maximum of 12 bonds
>
> I wonder why would this be necessary? Is there anyway to turn it off?
>
> Thanks,
> Bin
> 

-- 
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