ADL: few AD4 questions on optimization and speed

Narender Singh Maan nsmaan at gmail.com
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:

   1.

   Are the automatically added polar hydrogens optimized(minimized) in
   some way in AD4 (for the macromolecule) before the docking? If not..
   2.

   Is there some way in which this can be done?
   3.

   *If we specify do_local_only (for e.g. =50) in DPF, what exactly is
   getting energy minimized?*
   1.

      *The macromolecule (before docking) or the*
      2.

      *docked complex?*
       4.

   *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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