[Dock-fans] Mysterious crash

Kaitlyn Hwang hwang at mcs.anl.gov
Thu Oct 27 12:36:58 PDT 2005

Can you debug with valgrind or any debugging tools to see what happens
when the app crash? Do you get a core dump? What is the error output?

I have been working Dock5 with parallel, and see the segfault when I put
in the bug patches 6&8. So I took those two patches out. It would run
correctly at first (with the patches in), but after awhile it would crash.
My time processed for the Dock5 (without the patches) is off, but at least
it has been able to process 100k ligands.


On Thu, 27 Oct 2005, Darrell Hurt wrote:

> Hi everyone,
> I'm using DOCK 5.2 on a Linux box P4-3GHz machine, 1 GB RAM. I'm working
> with the PubMed, the Sigma-Aldrich, and the Developmental Therapeutics
> Program/NCI databases in mol2 format. When I dock ATP (the natural
> substrate) into the defined docking site (grid spacing 0.3, 1100
> spheres), I get a good orientation and a reasonable score. When I dock
> any of the databases, DOCK will run with them for about 800 molecules
> and then crash. "Unlimiting" the memory does not help. I then ran
> DBfilter 2.2.8 on the pubmed database, which increased the size of the
> database from ~135 MB to ~150 MB. When I dock with this database, I can
> process ~6400 molecules before the crash.
> Any hints?
> Thanks,
> Darrell
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