VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Feb 03 2007 - 06:31:49 CST

hi! the sidechain selection keyword had a memory leak. please try a
1.8.6 beta version. axel.

On 2/2/07, Arneh Babakhani <ababakha_at_mccammon.ucsd.edu> wrote:
> 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???
>
> Thanks,
>
> Arneh
>
>
>
> 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
> > 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
> >>
> >
> >
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.