VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Mon Feb 05 2007 - 10:59:04 CST

Hi John,

Yes, using index does indeed cure my problem, so that's what it was. Ok,
look forward to getting the new release of VMD!

Thanks,

Arneh

John Stone wrote:
> 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.
>>>
>>>
>
>