VMD-L Mailing List

From: zhngbn_at_gmail.com
Date: Tue Apr 21 2009 - 23:48:30 CDT

Hi, John:

Thanks a lot for your comment.

I'm actually trying to visualize some of the harmonic restraints applied
for a particular atom.

Thank,
Bin

On Apr 21, 2009 9:44pm, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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