ADL: few AD4 questions on optimization and speed

Narender Singh Maan nsmaan at
Thu Nov 29 11:57:43 PST 2007

Dear AD users,

I have some questions about autodock4 for which i tried/searched to find
answers, but was wondering if someone can please give me some more insights
on them:


   Are the automatically added polar hydrogens optimized(minimized) in
   some way in AD4 (for the macromolecule) before the docking? If not..

   Is there some way in which this can be done?

   *If we specify do_local_only (for e.g. =50) in DPF, what exactly is
   getting energy minimized?*

      *The macromolecule (before docking) or the*

      *docked complex?*

   *Speed: I have a small ligand (22 atoms, 5 atom types and 2
   torsionals) which i docked in a grid box of 60.60.60 and spacing of
   0.375Ang. With 100 ga_run and 150 ga_pop_size (rest all default
   GA-LGA) it took 53 CPU min to finish the calculations (My machine is
   Intel(R) Core(TM)2 CPU 6600 @ 2.40GHz). Is this value normal? (With
   this speed won't it take a very long time to do (for e.g.) say a
   100,000 compound library of small molecules)! *

*Thank you*

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