Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-31.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress nothing to compress du2.csh script updated ligand processing MakeDOCK 2.0, modified by J.Irwin and M.Mysinger. Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid5/people/mysinger/xyz/dockenv. Creating binding-site residue list Creating molecular surface real 1m16.490s user 0m0.180s sys 0m0.122s Creating sphgen spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 0: 913 spheres. 68. 68. 68. 68. 68. 68. 68. 68. 68. 69. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 74. 74. 74. 74. 74. 74. 77. 77. 83. 83. 83. 83. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 171. 171. 179. 179. 179. 182. 189. 189. 189. 196. 196. 198. 198. 198. 198. 198. 198. 198. 198. 202. 202. 202. 202. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 223. 227. 227. 227. 227. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 244. 244. 244. 244. 244. 363. 363. 366. 366. 366. 366. 366. 366. 366. 369. 369. 369. 369. 369. 369. 370. 370. 370. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 377. 377. 377. 377. 377. 379. 383. 383. 383. 383. 383. 383. 383. 383. 383. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 388. 388. 388. 388. 389. 389. 411. 599. 601. 601. 601. 601. 601. 602. 602. 602. 602. 602. 602. 602. 608. 608. 613. 615. 615. 615. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 620. 623. 623. 623. 623. 623. 623. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 631. 631. 631. 631. 631. 631. 631. 633. 633. 633. 633. 633. 633. 638. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 641. 641. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 939. 939. 939. 939. 940. 940. 940. 940. 940. 940. 940. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 954. 954. 954. 955. 955. 955. 955. 955. 955. 955. 955. 955. 966. 966. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 969. 969. 969. 969. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 973. 976. 976. 976. 978. 978. 978. 978. 978. 979. 979. 979. 979. 979. 979. 979. 979. 981. 985. 985. 985. 987. 987. 987. 987. 987. 987. 987. 987. 987. 987. 988.1002.1002.1002.1002.1121.1121.1121.1124.1127.1127.1127.1127.1128.1128.1128.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1135.1136.1136.1140.1140.1140.1140.1140.1140.1141.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1146.1146.1146.1146.1146.1147.1147.1149.1149.1149.1149.1149.1155.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1372.1372.1372.1373.1373.1374.1374.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1378.1381.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1396.1396.1396.1397.1397.1397.1397.1397.1397.1398.1398.1399.1414.1414.1414.1414.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.1422.FORTRAN STOP Converting ligand atoms to spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 14 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14.FORTRAN STOP Adding essential hydrogens to receptor #@jens_hydrogens.csh rec.pdb Generating matching spheres for delphi Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 120 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.9091.9092.9093.9094.9095.9096.9097.9098.9099.9100.9101.9102.9103.9104.9105.9106.9107.9108.9109.9110.9111.9112.9113.9114.9115.9116.9117.9118.9119.9120.FORTRAN STOP Generating faster matching2 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 45 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.FORTRAN STOP Coloring matching spheres Generating slower matching3 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 60 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.FORTRAN STOP Coloring matching spheres Adding spheres to electrostatic grid Creating DelPhi electrostatic grid real 1m50.367s user 0m27.108s sys 0m0.863s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m43.877s user 0m24.637s sys 0m0.698s Creating box around spheres Creating chemgrid maps real 0m41.436s user 0m11.724s sys 0m0.260s Atomic solvent excluded volume calculations underway FORTRAN STOP real 56m41.715s user 19m22.534s sys 0m0.353s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. Stop before docking.