[Dock-fans] Segmentation fault error

Kimberly Stieglitz stieglit at bc.edu
Fri Aug 12 07:45:59 PDT 2005

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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dock.in
Type: application/x-macbinary
Size: 5760 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050812/34f927e7/dock.bin
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test_rdz_dock5.out
Type: application/octet-stream
Size: 63292 bytes
Desc: not available
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20050812/34f927e7/test_rdz_dock5.obj

More information about the Dock-fans mailing list