From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 02 2007 - 16:21:44 CST

Arneh,
  This is typically caused by an improperly written script that
creates atom selections in a loop but does not delete them. You should
check and make sure that within all loops in your code, any place
you have a:
# inside loop
  set sel [atomselect $foo $bar]

You should also have a matching:
# inside loop
  $sel delete

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 02, 2007 at 02:16:04PM -0800, Arneh Babakhani wrote:
> Hi,
>
> I'm trying a run a script in vmd, in which I load up some trajectories
> and then calculate an RMSD. It worked just fine the first few times, but
> now it's crashing out on me, giving an error:
>
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
> Abort
>
>
> Any ideas what's causing this? I doubt its a VMD issue or a problem with
> my script, b/c it ran fine before. A computer issue? Need to reboot?
> (would rather not).
>
> Thanks,
>
> Arneh

-- 
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