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 0m2.404s user 0m0.459s sys 0m0.287s 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 0:1361 spheres. 68. 69. 69. 69. 69. 69. 69. 69. 69. 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. 75. 75. 75. 76. 76. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 197. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 226. 227. 227. 228. 228. 228. 228. 229. 231. 243. 244. 244. 244. 244. 244. 244. 244. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 347. 348. 348. 348. 348. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 358. 359. 361. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 364. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 370. 370. 370. 370. 370. 371. 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. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 379. 380. 384. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 387. 387. 387. 387. 389. 389. 389. 389. 389. 390. 390. 390. 391. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 393. 397. 397. 397. 398. 398. 398. 398. 399. 399. 399. 401. 403. 403. 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. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 412. 412. 412. 412. 425. 566. 570. 570. 571. 571. 571. 572. 572. 572. 572. 591. 591. 591. 591. 591. 591. 591. 591. 600. 602. 602. 602. 603. 603. 603. 603. 603. 603. 603. 604. 604. 604. 605. 609. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 621. 621. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 632. 634. 634. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 657. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 667. 667. 667. 667. 667. 667. 669. 669. 669. 669. 670. 670. 670. 670. 670. 673. 824. 824. 824. 824. 824. 824. 824. 827. 827. 827. 829. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 833. 833. 833. 834. 842. 842. 842. 842. 843. 843. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 930. 930. 930. 930. 941. 941. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 967. 967. 967. 967. 967. 967. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 978. 978. 979. 979. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 985. 986. 986. 986. 987. 988. 988. 988. 988. 988. 988. 988. 988. 989.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1008.1008.1008.1013.1013.1013.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1017.1018.1018.1019.1019.1019.1020.1105.1108.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1117.1117.1117.1117.1117.1119.1119.1120.1120.1120.1120.1122.1122.1122.1125.1125.1125.1125.1125.1125.1125.1125.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1129.1129.1129.1130.1130.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1136.1136.1136.1137.1137.1137.1138.1138.1138.1141.1141.1141.1141.1141.1141.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1147.1147.1148.1148.1148.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1155.1155.1156.1156.1156.1156.1156.1158.1158.1158.1159.1159.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1170.1170.1170.1170.1170.1170.1170.1171.1171.1171.1184.1184.1184.1202.1202.1205.1205.1205.1205.1205.1205.1205.1206.1206.1206.1206.1207.1324.1328.1328.1328.1328.1328.1328.1328.1328.1328.1329.1330.1330.1330.1330.1330.1330.1330.1345.1349.1349.1349.1349.1349.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1362.1363.1363.1363.1363.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1385.1385.1390.1390.1390.1391.1392.1392.1392.1392.1392.1392.1392.1392.1399.1399.1400.1400.1400.1400.1400.1400.1400.1415.1415.1421.1421.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1425.1425.1425.1425.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1429.1431.1431.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: 45 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.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 0m34.222s user 0m28.699s sys 0m0.918s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m46.199s user 0m28.531s sys 0m0.996s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m50.629s user 0m49.252s sys 0m0.410s Atomic solvent excluded volume calculations underway FORTRAN STOP real 33m24.726s user 33m21.390s sys 0m0.525s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 124 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.