VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Mar 24 2007 - 00:52:55 CDT

Hi,
  Mary, which version of VMD are you running, how many atoms were
in the PDB file, and how much memory does your computer have?
>From the information you've provided it seems that the evaporated
waters probably caused an unusually large spatial acceleration
data structure to be allocated, exceeding the amount of memory
available on your system, and causing an internal malloc() error,
and a segmentation fault to occur. All recent versions of VMD contain
code to prevent this type of thing from occuring, but you may
have found a new case that gets past these safety tests somehow.
If you can tell me more about your machine and the PDB file you're
loading, I should be able to either provide you with a workaround, or
else give you a new build that eliminates this problem once I know
for sure how/why it is occuring. I'd be happy to test loading your
PDB file if you gzip it and email it to me (send to vmd_at_ks.uiuc.edu
and not to the vmd-l mailing list if you're able to provide me
your file for examination).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 23, 2007 at 10:40:18PM -0400, Mary Lowe wrote:
> Hello,
> I would like to read a pdb file, but I get the following error message:
>
> vmd > Info) Using plugin pdb for structure file /Users/mary/CHARMM/arab6001_fix.pdb
> Info) Using plugin pdb for coordinates from file /Users/mary/CHARMM/arab6001_fix.pdb
> Info) Determining bond structure from distance search ...
> VMD(27128,0xa000ed68) malloc: *** vm_allocate(size=996216832) failed (error code=3)
> VMD(27128,0xa000ed68) malloc: *** error: can't allocate region
> VMD(27128,0xa000ed68) malloc: *** set a breakpoint in szone_error to debug
> Segmentation fault
>
> The file contains water molecules of which a few have evaporated. I rewrote the coordinates of the evaporated molecules so that they look like they are still present in the main structure.
>
> Can you explain what the error message means and how to correct the problem? Thanks. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078