bezek:~/ng/mm> cat dock.pln
parameter database_name label "database_name" text select oneof "aldrich" "maybridge" "maybridge_300" "asinex_egc" "asinex_epc" "asinex_pre" "available_chemicals_directory" "inter_bioscreen_s" "inter_bioscreen_n" "inter_bioscreen_n_300" "inter_bioscreen_n_500" "biomolecular_research_institute" "molecular_science" "molecular_diversity_preservation" "national_cancer_institute" "IGF_HITS" "aldrich_300" "molecular_science_500" "APP" "ECE" default "aldrich_300";
parameter PDB_SERVER text default "bezek.dstc.monash.edu.au";
parameter PDB_PORT_NO text default "5001";
parameter flexible_ligand text default "yes";
parameter orient_ligand text default "yes";
parameter score_ligand text default "yes";
parameter minimize_ligand text default "yes";
parameter multiple_ligands text default "no";
parameter random_seed integer default 7;
parameter anchor_search text default "no";
parameter torsion_drive text default "yes";
parameter clash_overlap float default 0.5;
parameter conformation_cutoff_factor integer default 5;
parameter torsion_minimize text default "yes";
parameter match_receptor_sites text default "yes";
parameter random_search text default "no";
parameter automated_matching text default "yes";
parameter ligand_centers text default "no";
parameter maximum_orientations integer default 100;
parameter write_configurations text default "yes";
parameter rank_orientations text default "yes";
parameter rank_orientation_total integer default 25;
parameter write_configuration_total integer default 25;
parameter intramolecular_score text default "yes";
parameter intermolecular_score text default "yes";
parameter gridded_score text default "yes";
parameter grid_version integer default 4;
parameter bump_filter text default "yes";
parameter bump_maximum integer default 3;
parameter contact_score text default "yes";
parameter contact_cutoff_distance float default 4.5;
parameter contact_clash_overlap float default 0.75;
parameter contact_clash_penalty float default 50;
parameter chemical_score text default "yes";
parameter energy_score text default "yes";
parameter energy_cutoff_distance integer default 10;
parameter distance_dielectric text default "yes";
parameter dielectric_factor integer default 4;
parameter attractive_exponent integer default 6;
parameter repulsive_exponent integer default 12;
parameter atom_model text default "a";
parameter vdw_scale integer default 1;
parameter electrostatic_scale integer default 1;
parameter contact_minimize text default "yes";
parameter chemical_minimize text default "yes";
parameter energy_minimize text default "yes";
parameter initial_translation integer default 1;
parameter initial_rotation float default 0.1;
parameter initial_torsion integer default 10;
parameter maximum_iterations integer default 100;
parameter contact_convergence float default 0.1;
parameter chemical_convergence float default 0.1;
parameter energy_convergence float default 0.1;
parameter maximum_cycles integer default 1;
parameter receptor_site_file text default "ece.sph";
parameter score_grid_prefix text default "ece";
parameter ligand_number integer range from 1 to 2000 step 1;
task nodestart
      copy ./parameter/vdw.defn node:.
      copy ./parameter/chem.defn node:.
      copy ./parameter/chem_score.tbl node:.
      copy ./parameter/flex.defn node:.
      copy ./parameter/flex_drive.tbl node:.
      copy ./dock_inputs/get_molecule node:.
      copy ./dock_inputs/dock_base node:.
endtask
task main
           node:substitute dock_base dock_run
           copy node:dock_run ./results/dock_run.$jobname
           node:substitute get_molecule get_molecule_fetch
           node:execute sh ./get_molecule_fetch
           node:execute $HOME/bin/dock.$OS -i dock_run -o dock_out
           copy node:dock_out ./results/dock_out.$jobname
           copy node:dock_cnt.mol2 ./results/dock_cnt.mol2.$jobname
           copy node:dock_chm.mol2 ./results/dock_chm.mol2.$jobname
           copy node:dock_nrg.mol2 ./results/dock_nrg.mol2.$jobname
endtask
task rootfinish
                #execute /home/enfuzion/final_scripts/collate.pl > results
endtask