[ USE Enfuzion/cluster to create RunFile from Plan file: RUN FILE CREATED FROM dock.pln FILE for 200 ligands by updating: parameter ligand_number integer range from 1 to 200 step 1; ] bezek:~/ng/mm> cat dock200.run set rootfiles delete; set nodefiles delete; 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_ece/get_molecule node:. copy ./dock_inputs_ece/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 variable database_name constant "aldrich_300"; variable PDB_SERVER constant "bezek.dstc.monash.edu.au"; variable PDB_PORT_NO constant "5001"; variable flexible_ligand constant "yes"; variable orient_ligand constant "yes"; variable score_ligand constant "yes"; variable minimize_ligand constant "yes"; variable multiple_ligands constant "no"; variable random_seed constant "7"; variable automated_matching constant "yes"; variable anchor_search constant "no"; variable torsion_drive constant "yes"; variable clash_overlap constant "0.5"; variable conformation_cutoff_factor constant "5"; variable torsion_minimize constant "yes"; variable match_receptor_sites constant "yes"; variable random_search constant "no"; variable ligand_centers constant "no"; variable maximum_orientations constant "100"; variable write_configurations constant "yes"; variable rank_orientations constant "yes"; variable rank_orientation_total constant "25"; variable write_configuration_total constant "25"; variable intramolecular_score constant "yes"; variable intermolecular_score constant "yes"; variable gridded_score constant "yes"; variable grid_version constant "4"; variable bump_filter constant "yes"; variable bump_maximum constant "3"; variable contact_score constant "yes"; variable contact_cutoff_distance constant "4.5"; variable contact_clash_overlap constant "0.75"; variable contact_clash_penalty constant "50"; variable chemical_score constant "yes"; variable energy_score constant "yes"; variable energy_cutoff_distance constant "10"; variable distance_dielectric constant "yes"; variable dielectric_factor constant "4"; variable attractive_exponent constant "6"; variable repulsive_exponent constant "12"; variable atom_model constant "a"; variable vdw_scale constant "1"; variable electrostatic_scale constant "1"; variable contact_minimize constant "yes"; variable chemical_minimize constant "yes"; variable energy_minimize constant "yes"; variable initial_translation constant "1"; variable initial_rotation constant "0.1"; variable initial_torsion constant "10"; variable maximum_iterations constant "100"; variable contact_convergence constant "0.1"; variable chemical_convergence constant "0.1"; variable energy_convergence constant "0.1"; variable maximum_cycles constant "1"; variable receptor_site_file constant "ece.sph"; variable score_grid_prefix constant "ece"; variable ligand_number index 0 list "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60" "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72" "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84" "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96" "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" "120" "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131" "132" "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143" "144" "145" "146" "147" "148" "149" "150" "151" "152" "153" "154" "155" "156" "157" "158" "159" "160" "161" "162" "163" "164" "165" "166" "167" "168" "169" "170" "171" "172" "173" "174" "175" "176" "177" "178" "179" "180" "181" "182" "183" "184" "185" "186" "187" "188" "189" "190" "191" "192" "193" "194" "195" "196" "197" "198" "199" "200"; indexcount 1 jobs 001 0 002 1 003 2 004 3 005 4 006 5 007 6 008 7 009 8 010 9 011 10 012 11 013 12 014 13 015 14 016 15 017 16 018 17 019 18 020 19 021 20 022 21 023 22 024 23 025 24 026 25 027 26 028 27 029 28 030 29 031 30 032 31 033 32 034 33 035 34 036 35 037 36 038 37 039 38 040 39 041 40 042 41 043 42 044 43 045 44 046 45 047 46 048 47 049 48 050 49 051 50 052 51 053 52 054 53 055 54 056 55 057 56 058 57 059 58 060 59 061 60 062 61 063 62 064 63 065 64 066 65 067 66 068 67 069 68 070 69 071 70 072 71 073 72 074 73 075 74 076 75 077 76 078 77 079 78 080 79 081 80 082 81 083 82 084 83 085 84 086 85 087 86 088 87 089 88 090 89 091 90 092 91 093 92 094 93 095 94 096 95 097 96 098 97 099 98 100 99 101 100 102 101 103 102 104 103 105 104 106 105 107 106 108 107 109 108 110 109 111 110 112 111 113 112 114 113 115 114 116 115 117 116 118 117 119 118 120 119 121 120 122 121 123 122 124 123 125 124 126 125 127 126 128 127 129 128 130 129 131 130 132 131 133 132 134 133 135 134 136 135 137 136 138 137 139 138 140 139 141 140 142 141 143 142 144 143 145 144 146 145 147 146 148 147 149 148 150 149 151 150 152 151 153 152 154 153 155 154 156 155 157 156 158 157 159 158 160 159 161 160 162 161 163 162 164 163 165 164 166 165 167 166 168 167 169 168 170 169 171 170 172 171 173 172 174 173 175 174 176 175 177 176 178 177 179 178 180 179 181 180 182 181 183 182 184 183 185 184 186 185 187 186 188 187 189 188 190 189 191 190 192 191 193 192 194 193 195 194 196 195 197 196 198 197 199 198 200 199 endjobs