AW: vmd-l: Error: Maximum number of bonds exceeded

From: Norman Geist (
Date: Mon Sep 09 2013 - 01:06:38 CDT



not much information, but I’ll try. As you assume it to be an error, your
structure doesn’t contain more bonds than VMD can cope withm, right!?
Therefore I assume that your structure or pdb is garbage as it generates
lots of superimposed molecules which will lead the VMD “autobond” generator
to bind all these atoms together, as the pdb doesn’t contain bond
information. A common reason for this is either molecule copies with same
coordinates or a pdb that has broken columns due to big numbers for index,
resid or coordinates, what causes many atoms to appear at the same location.
If you already have a psf/prmtop for your structure, loading it first should
prevent the autobond feature from breaking when loading pdb into it. Try and
check if everthing appears right, otherwise, check the columns of your pdb.
Additionally, you should have mentioned if you use amber or charmm, as for
example xleap can’t handle coordinates bigger 999.9999 atom numbers bigger
99999 and resids bigger 9999 and would lead to the behavior you described.


Good luck


Norman Geist.


Von: [] Im Auftrag von
Orsolya Karácsony
Gesendet: Samstag, 7. September 2013 20:30
Betreff: vmd-l: Error: Maximum number of bonds exceeded



I have tried to open two different files that appear fine in another
instance of VMD,

on another computer, I got this error. I have Win XP wih .NET 4.0, the
latest SDK,

and an earlier, but extensively tested version of OpenCV. I have removed

downloaded the installer again, insalled it again - same thing. Please

Thanks a lot,


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:38 CST