ADL: error message in autodock4

Garrett M. Morris garrett at
Wed Mar 26 18:49:20 PDT 2008

Dear Borries,

On 26 Mar, 2008, at 5:53 am, Borries Demeler wrote:
> 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
> ________________________________________________
> --- ADL: AutoDock List  ---  
> ---

This has been fixed in the current unreleased version of AutoDock; in  
the meantime, the workaround for these problem molecules is to use  
"unbound 0.0" instead of "compute_unbound_extended" in these  
particular ligand's DPFs.  (Note: you might also try adding  
"include_1_4_interactions" to the start of the DPFs, this also might  
resolve these cases.)

Please accept my apologies for any inconvenience this may have caused.


Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at
La Jolla,  CA 92037-1000,  USA.

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