ADL: slow docking time

Osmany Guirola osmany_guirola at yahoo.com
Tue Oct 2 14:25:02 PDT 2007


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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