ADL: slow docking time

L. Michel Espinoza-Fonseca mef at ddt.biochem.umn.edu
Tue Oct 2 14:44:05 PDT 2007


Hi Osmany,

I think that an average of 10 mins/run is quite good (if you have a
set of ~2000 compounds, it means that it'll take you ~14 days to
screen all of them).

If you want to reduce the time of your computations, you could reduce
the number of energy evaluations to 250,000, for example. Be aware
that this could also strongly influence the quality of your docking
results.

Cheers,
Michel

2007/10/2, Osmany Guirola <osmany_guirola at yahoo.com>:
> Hi
>
> i do a virtual screening experiment with the diversity set of NCI
> ~1990 molecules
> the average was 10minutes/compound
> i think this is a very long  time if i want make a biggwer screening.
> this is my .dpf file
>  should change some parameters?
> which?
>
> outlev 1                             # diagnostic output level
> intelec                              # calculate internal electrostatics
> seed pid time                        # seeds for random generator
> ligand_types A C HD N OA             # atoms types in ligand
> fld receptor.maps.fld                # grid_data_file
> map receptor.A.map                   # atom-specific affinity map
> map receptor.C.map                   # atom-specific affinity map
> map receptor.HD.map                  # atom-specific affinity map
> map receptor.N.map                   # atom-specific affinity map
> map receptor.OA.map                  # atom-specific affinity map
> elecmap receptor.e.map               # electrostatics map
> desolvmap receptor.d.map             # desolvation map
> move 61806.pdbqt                     # small molecule
> about 1.9943 -1.7364 -0.7233         # small molecule center
> tran0 random                         # initial coordinates/A or random
> quat0 random                         # initial quaternion
> ndihe 6                              # number of active torsions
> dihe0 random                         # initial dihedrals (relative) or random
> tstep 2.0                            # translation step/A
> qstep 50.0                           # quaternion step/deg
> dstep 50.0                           # torsion step/deg
> torsdof 5 0.274000                   # torsional degrees of freedom and coefficient
> rmstol 2.0                           # cluster_tolerance/A
> extnrg 1000.0                        # external grid energy
> e0max 0.0 10000                      # max initial energy; max number of retries
> ga_pop_size 150                      # number of individuals in population
> ga_num_evals 1750000                 # maximum number of energy evaluations
> ga_num_generations 27000             # maximum number of generations
> ga_elitism 1                         # number of top individuals to survive to next generation
> ga_mutation_rate 0.02                # rate of gene mutation
> ga_crossover_rate 0.8                # rate of crossover
> ga_window_size 10                    #
> ga_cauchy_alpha 0.0                  # Alpha parameter of Cauchy distribution
> ga_cauchy_beta 1.0                   # Beta parameter Cauchy distribution
> set_ga                               # set the above parameters for GA or LGA
> sw_max_its 300                       # iterations of Solis & Wets local search
> sw_max_succ 4                        # consecutive successes before changing rho
> sw_max_fail 4                        # consecutive failures before changing rho
> sw_rho 1.0                           # size of local search space to sample
> sw_lb_rho 0.01                       # lower bound on rho
> ls_search_freq 0.06                  # probability of performing local search on individual
> set_sw1                              # set the above Solis & Wets parameters
> compute_unbound_extended             # compute extended ligand energy
> ga_run 20                            # do this many hybrid GA-LS runs
> analysis                             # perform a ranked cluster analysis
>
>
>
>
>
>
>
>
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