ADL: error message in autodock4

Borries Demeler demeler at biochem.uthscsa.edu
Wed Mar 26 05:53:49 PDT 2008


Hi,

I didn't search your archives to see if this was mentioned before,
but I didn't see it listed in your faqs...

When screening a large library autodock4 fails to converge in
about 0.5% of the compounds listed. In those cases, I see the 
message:

NOTE: All energies are equal in population; re-initializing....

endlessly repeated in the log file, which grows very large. I am not
sure if this is a bug in the initialization, but in my opinion the 
program should exit in such a case more gracefully. I never see this
string in any of successful fits, which would indicate to me that
the program has hit en error condition from which it can't escape.
So my suggestion would be to better deal with the initialization, or
change the output message to better reflect the true error condition,
whatever it is.

I should also mention that some of the compounds miraculously do
converge if I just restart the program. I don't know how the program
works, but my interpretation of this symptom would be that you use
time to initialize the random seed of your GA, and then when I restart
it I get a better initialization. However, when the program gets stuck
in this loop, even though it says that it reinitializes, it never actually
does. Does that seem plausible?

Thanks, -Borries 


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