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Why do the results differ when multiple dockings are done with the same input?

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This FAQ applies to: AutoDock 3, AutoDock 4

Multiple docking calculations are specified in a docking parameter file using one of the following keywords: 'ga_run', 'do_local_only' or 'runs' plus 'simanneal'. In general, the results will differ between dockings when using the same input.

1. AutoDock uses a random number generator to create new poses for the ligand
during its search. 

2. The random number generator used by AutoDock produces a sequence of random
numbers based on two initial seeds. The new conformations for the search are
created using this sequence of random numbers to set location, orientation and
torsion values.

3. The default values for these two seeds are 'pid' and 'time'. Process id
and time vary between AutoDock calculations.

4. Therefore, the sequence of random numbers is different between different
AutoDock calculations. As a result, the 'search' is encountering a different
set of random conformations. Thus the results differ.

Please note, it is possible to specify the seeds explicitly. In this case,
multiple AutoDock calculations should give the same, albeit restricted, results.

A separate consideration is that convergence of the docked results is an
indication of the thoroughness of the search.  If the dockings in a single
AutoDock calculation vary greatly, possibly the the search hasn't been
thorough enough to find the minima in the energy landscape for a particular
docking problem.  In this case, the search may need to be extended by
increasing the number of energy evaluations or the number of generations.

by Ruth Huey last modified 2009-07-06 11:18

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