[Dock-fans] ERROR while runing the demo and other issues

Terry Lang terry at cgl.ucsf.edu
Tue Jul 12 17:38:28 PDT 2005

Dear Amit,

          For your first issue, if you are generating chemical grids 
with the program "grid," you need to remove the entry
name        null
definition    *

from the chem.defn file.  This entry in the parameter file is not 
backwards compatible with the "grid" program.  That being said, there is 
no function in "dock5" that reads in chemical grids.  Chemical scoring 
did not enhance success rates and we have decided not to reimplement it 
in the new version of DOCK.   We will be removing that capability from 
the "grid" program in the next release to remove confusion. 
          For your ligands, I am not sure what the problem is exactly.  
Could you send a copy of your ligand files and your dock input files?  I 
can take a look and see if I can figure out what is going on.


Amit wrote:

> Dear dock-fans,
> I'm new at the docking field ... and with using DOCK.
> I'm currently using DOCK 5.2.
> I have two major problems:
> --------
> 1) I've encountered this error message when I tried to run the demo 
> "grid.in" with the modification of 'chemical matching' option set to 
> 'yes':
> "ERROR get_chemical_labels: <null> specified if 
> /software/graphics/DOCK/dock.5.2_Linux/parameters/chem.defn"
> This error message has appeared when I tried to calculate my receptor 
> grid with the same modification in the "grid.in" - which led me to try 
> the same thing with the demo.
> DOCK works fine with my actual receptor-ligand system (in some cases - 
> see the second section) when the chemical matching is not used for the 
> grid calculation.
> What might be the problem ?
> --------
> 2) I have been getting the 'segmentation fault' message  for a lot of 
> my runs. To  isolate the problem I've used the demo's "dock.in" file 
> and kept going with it till I've reached the point were DOCK is able 
> to finish its calculations.
> My ligands are peptides  with inter-strand disulfide bonds.
> Docking was only made possible when I had broken these bonds and 
> turned the cystine into 2 separate cysteines. I have changed the CYS 
> to CYX (back and forth) and it didn't resolve the segmentation fault.
> What does this error message is meant to say in my case. Is it just 
> impossible to dock this peptide if regarding it as a "flexible ligand" ?
> --------
> Sorry for the length of things written here and thanks for your time 
> and effort, of course - in advance,
> Amit
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> Dock-fans at docking.org
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P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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