VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 05 2007 - 10:04:31 CST

Arneh,
  If using the index selection cures your problem, then you're indeed
running a version that had a memory leak in the "sidechain" selection
keyword which is fixed in the newest test versions. We'll have a new
official VMD release soon, if you would rather not bother with the
test versions.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Feb 04, 2007 at 07:58:19PM -0800, Arneh Babakhani wrote:
> Hmmm, interesting. Ok, I was able to circumvent the problem. When I
> select, "resname TRP and sidechain", I get the error. But when I select
> "index 6 to 21" (the atoms of the indole ring), it works fine.
> Interesting . . . ok, thanks,
>
>
> > 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.
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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