[Dock-fans] Mysterious crash

Darrell Hurt darrellh at niddk.nih.gov
Thu Oct 27 10:56:55 PDT 2005

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?


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