[Dock-fans] Segmentation fault error

Terry Lang terry at cgl.ucsf.edu
Fri Aug 12 13:55:10 PDT 2005

Dear Kimberly,

    There were some other people having a similar problem with large 
databases.  It turned out that they were using sphere files that 
contained multiple clusters, which threw off the sphere reader 
internally but did not warn the user.  This particular issue can be 
fixed by using a sphere file with only cluster or by applying the 
appropriate bug fix from the web site.  If you are still having problems 
with your database, please send me the tarred files and I will take a 
look (NOTE:  Please send these files to me only so as not to overwhelm 
everyone's Inbox).


Kimberly Stieglitz wrote:

>Hi all:  
>I am a new user of dock5.  I have been using dock5 to dock small molecules from zinc database files
>in an allosteric binding pocket of my protein.  I am able to select spheres using sphere_selector to build the 
>binding pocket.  I am able to make a box and grids without a problem and the resulting molecular surface, box
>and selected spheres looks reasonable when displayed in Chimera.
>I am also able to run a  dock.in script with a small number of input.mol2 files.  My problem is we have split up
>some of the zinc database files into 10 MB files.  When running these mol2 input files  I am getting Segmentation fault error.  What is really confusing is that is is not the same point in each file--for some I can get ~ 800 mol2 
>files written out for other input files only ~ 100-200 mol2 files.  We have tested the dock.in script on another
>protein which has much higher output yields than this without the segmentation fault.
>Any advice you can offer is greatly appreciated.
>Kimberly Stieglitz
>Boston College Chemistry Department
>Merkert Chemistry Center
>Chestnut Hill MA
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


More information about the Dock-fans mailing list