ADL: flexible sidechains dramatically affected my analysis times
trott at scripps.edu
Mon Nov 25 19:17:14 PST 2013
That sounds about right. When there are many movable atoms, the run
time (for a given exhaustiveness setting) is roughly quadratic in the
number of movable atoms, i.e. if you go e.g. from 50 atoms to 250
atoms, things will get about 25 times slower IN ADDITION to the
scoring function facing a tougher problem of discriminating among many
more viable alternatives and the search algorithm needing to search
more thoroughly. The latter problem can be alleviated by increasing
the exhaustiveness, at the expense of slowing things down even more.
Please see http://mgl.scripps.edu/forum/viewtopic.php?f=12&t=235 for
some relevant recommendations.
On Mon, Nov 25, 2013 at 6:58 PM, Dennis N Bromley <dbromley at uw.edu> wrote:
> Hi everyone,
> I understand that flexible side chains necessitate more computations. But
> my analysis time for a given ligand went from ~30 second to ~30 minutes.
> Is this normal? I am using 15-20 flexible side chains in the pocket of a
> ~200 residue protein.
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Oleg Trott, Ph.D. (Columbia University)
Staff Scientist in the Olson Lab
The Scripps Research Institute
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