VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Sun Feb 04 2007 - 21:58:19 CST

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.
>