[Dock-fans] ERROR while runing the demo and other issues
amit.mor at weizmann.ac.il
Tue Jul 12 09:35:59 PDT 2005
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
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
What might be the problem ?
2) I have been getting the 'segmentation fault' message for a lot of my
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
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,
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