5. Template files
The template files are used by GriDock to prepare the AutoDock 4 input files.
They are placed in the ...\VEGA ZZ\Data\Autodock directory (or .../vega/Data/Autodock
directory for the Linux version) and have the .dpf file extension.
The template file can be selected by -t option.
The template files are standard AutoDock 4 files in which special tags are
present that are substituted by GriDock with parameters that are specific for
each molecule to screen as shown in the following table:
| Tag name | Description |
| %ATOMTYPES% | AMBER atom types of the ligand. Each type is separated by a space. |
| %CENTGEO% | Ligand center (format: X Y Z). |
| %DESOLVMAPFILE% | Desolvation map (e.g. RECEPTOR.d.map). |
| %ELECMAPFILE% | Electrostatic map (e.g. RECEPTOR.e.map). |
| %FLDFILE% | Grid data file (e.g. RECEPTOR.maps.fld). |
| %LIGAND% | Ligand file name with full path. |
| %MAPS% | List of the maps with the following format: map
RECEPTOR.ATMTYPE_1.map |
| %TORFLEXNUM% | Number of the flexible torsions. |
Each tag can be repeated more than one time in the template file.
This is a GriDock template example for virtual screening:
# # ***************************************** # **** GriDock template for AutoDock 4 **** # ***************************************** # # Default input file for virtual screening # outlev 1 # diagnostic output level intelec # calculate internal electrostatics seed pid time # seeds for random generator ligand_types %ATOMTYPES% # atoms types in ligand fld %FLDFILE% # grid_data_file %MAPS% elecmap %ELECMAPFILE% # electrostatics map desolvmap %DESOLVMAPFILE% # desolvation map move %LIGAND% # small molecule about %CENTGEO% # small molecule center tran0 random # initial coordinates/A or random quat0 random # initial quaternion ndihe %TORFLEXNUM% # 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 %TORFLEXNUM% 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 100000 # maximum number of energy evaluations (2500000, 50000) 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 10 # do this many hybrid GA-LS runs (10) analysis # perform a ranked cluster analysis