ADL: slow docking time

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Wed Oct 3 04:03:45 PDT 2007


Hi Osmany,

You might might be able to get by with sw_max_its at less than 300 (the local search takes 
up a significant fraction of the energy evaluations) while concurrently reducing 
ga_num_evals. Also, dockings of less flexible molecules will converge faster than dockings 
of more flexible molecules. 1750000 evals is more than you would need for ligands with 1-2 
torsions but probably not enough for ligands with 10 torsions. Is there any reasonably 
convenient way for you to prepare your dpfs with ga_num_evals tailored for each ligand in 
the diversity set (say ~250000 per torsion)?

Regards,

Mark

----- Original Message -----
From: Osmany Guirola <osmany_guirola at yahoo.com>
Date: Tuesday, October 2, 2007 4:36 pm
Subject: ADL: slow docking time
To: autodock <autodock at scripps.edu>


> 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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