From: Arneh Babakhani (
Date: Fri Feb 02 2007 - 20:04:29 CST

Hi John, thanks for the suggestion. I am aware of this problem. I've
made the correction.

But, I'm still getting the error. I'm just trying to plot out some
RMSDs. Everything works fine when I run the script to calculate the RMSD
of the entire peptide (that is when I set the selection to be the entire
peptide). But then I get the error when I try to do the same analysis
for one sidechain (in other words, just changing the selection). Rather
bizarre . . .

If there was something wrong with my script, it should fail always,
irrespective of the selection, no???



John Stone wrote:
> 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
> 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