From: John Stone (
Date: Wed Mar 24 2004 - 15:47:03 CST

  The problem here is that in absence of explicit bond information,
VMD is forced to "guess" which atoms are bonded using a simple
distance-based bond search heuristic. In many biomolecular cases
this works fairly well, but it doesn't work well for structures like yours.
I'm thinking about adding a GUI checkbox and new load command parameter to
defeat the auto-determination of bonds, though this won't help you in the
short term.

The errors you received while loading your structure should not have
been fatal, so it should be easy to use a script like the one I've
attached to null out any errant bonds you ended up getting.

Here's a simple script to zap all of the bonds within a particular
atom selection.

  John Stone

## Example script to delete all bonds within a group of selected atoms
## usage example:
## mol new 1ap9
## source deleteallbonds.tcl
## deleteallbonds top all

proc deleteallbonds { molid seltext } {
  set sel [atomselect $molid $seltext]
  set indexlist [$sel list]
  $sel delete

  foreach atom $indexlist {
    set sel [atomselect $molid "index $atom"]
    $sel setbonds {{}}
    $sel delete

On Wed, Mar 24, 2004 at 10:22:42AM -0700, Kooser, Ara S wrote:
> Hello,
> I am new to VMD. I was trying to bring in a 560 atom Au surface (xyz
> format) into VMD. I end up with the: to many bonds error. A member of the
> list suggested I convert the file to a .psf. I am unsure how to do this
> since I can't load the structure into VMD to convert it to a .psf. Thank
> you for your time.
> Ara Kooser

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