Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-1-40.c.bkslab.org du2 starts first try already in then inzinc count is 0 count is 0 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 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 0:1342 spheres. 281. 281. 281. 281. 281. 283. 283. 283. 284. 287. 287. 287. 287. 287. 287. 290. 292. 292. 292. 292. 292. 292. 295. 296. 296. 296. 296. 296. 296. 296. 296. 296. 296. 296. 297. 297. 297. 297. 297. 297. 297. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 298. 299. 299. 300. 300. 300. 300. 300. 300. 300. 300. 300. 300. 300. 300. 300. 300. 305. 305. 305. 305. 305. 305. 305. 306. 306. 306. 306. 306. 306. 306. 307. 307. 307. 307. 307. 307. 307. 307. 307. 307. 307. 310. 310. 311. 311. 311. 311. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 313. 313. 314. 314. 314. 314. 315. 321. 321. 321. 321. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 322. 324. 324. 324. 327. 327. 329. 329. 329. 329. 329. 329. 329. 329. 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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: 18 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. Adding essential hydrogens to receptor 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. 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. 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. Coloring matching spheres Adding spheres to electrostatic grid Creating DelPhi electrostatic grid Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid Creating box around spheres Creating chemgrid maps Atomic solvent excluded volume calculations underway Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys slept 360 waiting for decoys failed to get decoys