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 0m1.277s user 0m0.196s sys 0m0.183s 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 0:1541 spheres. 66. 66. 67. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 76. 76. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 172. 172. 182. 182. 183. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 223. 223. 223. 223. 223. 223. 226. 226. 226. 226. 227. 227. 227. 228. 228. 228. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 238. 238. 238. 238. 238. 238. 238. 238. 238. 243. 243. 243. 243. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 250. 250. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 259. 259. 260. 260. 260. 260. 261. 261. 261. 261. 261. 262. 262. 262. 262. 262. 262. 262. 262. 262. 347. 347. 348. 348. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 355. 359. 360. 362. 362. 362. 362. 362. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 368. 368. 368. 368. 368. 368. 368. 368. 369. 371. 372. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 376. 376. 376. 376. 376. 376. 376. 376. 379. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 385. 386. 386. 386. 387. 387. 387. 387. 387. 388. 389. 389. 389. 389. 389. 389. 390. 390. 390. 390. 391. 391. 392. 392. 392. 392. 392. 392. 392. 392. 392. 398. 398. 398. 398. 400. 401. 401. 401. 401. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 412. 412. 412. 412. 412. 412. 565. 565. 569. 569. 569. 569. 569. 569. 569. 569. 569. 569. 569. 569. 569. 569. 570. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 571. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 586. 590. 595. 599. 599. 599. 599. 599. 599. 599. 599. 601. 601. 601. 601. 601. 601. 602. 602. 602. 603. 608. 608. 613. 613. 613. 613. 614. 615. 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. 616. 616. 616. 616. 616. 616. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 623. 623. 623. 623. 623. 623. 623. 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. 630. 630. 630. 630. 630. 630. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 639. 639. 640. 640. 640. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 646. 655. 655. 655. 661. 661. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 665. 665. 665. 665. 665. 667. 667. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 669. 669. 669. 669. 669. 822. 822. 822. 825. 825. 825. 825. 825. 825. 825. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 831. 831. 840. 840. 840. 840. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 928. 928. 928. 928. 939. 939. 939. 939. 939. 939. 939. 953. 955. 955. 955. 955. 955. 955. 955. 955. 959. 965. 965. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 968. 968. 968. 968. 968. 968. 968. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 972. 975. 975. 976. 976. 976. 976. 976. 976. 976. 977. 977. 977. 977. 977. 977. 978. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 980. 982. 982. 982. 982. 983. 983. 984. 984. 984. 984. 984. 984. 986. 986. 986. 986. 986. 988. 999. 999.1000.1000.1000.1000.1000.1000.1006.1006.1006.1006.1006.1006.1006.1011.1011.1011.1013.1013.1013.1013.1013.1013.1013.1013.1013.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1016.1017.1017.1018.1018.1103.1109.1109.1109.1109.1109.1110.1110.1114.1117.1118.1118.1118.1118.1118.1120.1120.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1125.1126.1126.1126.1126.1126.1126.1127.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1138.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1145.1145.1146.1146.1146.1146.1146.1146.1146.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1153.1154.1154.1154.1154.1157.1157.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1168.1168.1168.1168.1170.1173.1173.1173.1173.1174.1174.1174.1174.1174.1174.1176.1177.1180.1180.1342.1342.1342.1355.1355.1355.1355.1355.1355.1355.1355.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1364.1369.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1374.1374.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1386.1386.1386.1386.1386.1386.1386.1387.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1395.1395.1396.1396.1396.1411.1416.1416.1417.1417.1418.1418.1418.1418.1418.1418.1418.1421.1421.1421.1421.1424.1424.1424.1424.1424.1424.1424.1425.1425.1425.1425.1425.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: 51 spheres. 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.FORTRAN STOP Adding essential hydrogens to receptor Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... Renaming polar hydrogens... 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 we had to cook * HD2* Creating DelPhi electrostatic grid real 0m32.226s user 0m28.538s sys 0m1.239s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m58.305s user 0m25.638s sys 0m0.963s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m18.162s user 0m10.086s sys 0m0.491s Atomic solvent excluded volume calculations underway FORTRAN STOP real 16m40.024s user 16m38.853s sys 0m0.081s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.