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 0m38.719s user 0m0.385s sys 0m0.259s 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 0:1646 spheres. 80. 80. 86. 86. 86. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 91. 91. 92. 92. 92. 92. 92. 92. 92. 92. 93. 93. 93. 93. 95. 95. 96. 96. 96. 96. 96. 96. 97. 97. 100. 105. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 107. 107. 107. 109. 113. 113. 113. 113. 116. 116. 116. 116. 116. 116. 117. 117. 117. 117. 117. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 122. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 124. 307. 307. 308. 308. 308. 308. 308. 308. 308. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 309. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 310. 327. 327. 327. 327. 328. 328. 328. 328. 328. 328. 328. 328. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 332. 332. 332. 332. 332. 332. 332. 333. 333. 333. 333. 333. 333. 333. 333. 333. 333. 333. 333. 334. 368. 368. 372. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 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. 402. 402. 402. 402. 402. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 406. 406. 406. 406. 406. 406. 406. 406. 407. 408. 408. 408. 408. 408. 408. 408. 409. 409. 409. 409. 409. 409. 409. 410. 410. 410. 410. 410. 419. 419. 419. 419. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 422. 422. 422. 422. 422. 422. 422. 422. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 427. 435. 435. 435. 435. 435. 435. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 436. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 689. 690. 690. 690. 690. 695. 695. 696. 696. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 697. 698. 698. 698. 698. 698. 698. 698. 698. 698. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 710. 717. 717. 717. 717. 718. 718. 718. 719. 719. 719. 719. 719. 719. 719. 719. 722. 723. 723. 723. 723. 723. 724. 724. 725. 726. 726. 726. 726. 726. 726. 726. 726. 726. 726. 726. 726. 726. 726. 906. 906. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 907. 916. 916. 916. 916. 920. 921. 921. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 924. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 927. 927. 927. 927. 927. 928. 928. 928. 929. 930. 930. 933. 933. 933. 933. 934. 934. 934. 934. 934. 935. 937. 937. 940. 940. 940. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 953. 953. 953. 953. 953. 953. 957. 962. 963. 963. 963. 964. 964. 964. 964. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 966. 966. 966. 966. 970. 970. 971. 971. 971. 971. 973. 973. 973. 973. 973. 973. 973. 973. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 983. 984. 984. 985. 985. 985. 985. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 987. 987. 987. 987. 987. 987. 988. 988. 988. 988. 988. 988.1185.1186.1186.1186.1186.1187.1188.1188.1188.1188.1188.1188.1188.1188.1188.1188.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1198.1198.1198.1198.1199.1203.1203.1203.1203.1211.1211.1211.1211.1211.1211.1211.1211.1211.1212.1212.1212.1212.1212.1212.1212.1212.1212.1212.1212.1212.1213.1219.1219.1219.1227.1227.1227.1227.1227.1227.1227.1227.1228.1228.1228.1228.1228.1228.1228.1228.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1232.1232.1232.1232.1232.1232.1232.1272.1272.1275.1275.1275.1275.1275.1275.1275.1275.1275.1275.1306.1306.1306.1306.1306.1309.1309.1309.1309.1309.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1311.1311.1311.1312.1312.1312.1312.1312.1312.1312.1312.1312.1314.1317.1317.1317.1317.1317.1317.1317.1317.1317.1317.1317.1317.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1319.1319.1319.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1324.1324.1324.1324.1324.1324.1324.1325.1326.1326.1326.1326.1326.1326.1326.1326.1327.1327.1327.1327.1327.1327.1327.1327.1328.1328.1328.1328.1328.1328.1330.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1333.1333.1333.1333.1333.1333.1333.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1337.1337.1337.1337.1337.1339.1339.1339.1339.1340.1340.1340.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1345.1345.1348.1349.1349.1350.1350.1350.1350.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1352.1352.1352.1352.1352.1354.1354.1354.1354.1354.1355.1355.1355.1356.1356.1356.1356.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1368.1368.1368.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1374.1374.1375.1375.1375.1375.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1383.1383.1383.1389.1390.1391.1391.1391.1391.1395.1395.1400.1400.1400.1400.1400.1400.1400.1400.1400.1401.1401.1402.1402.1402.1402.1402.1403.1403.1403.1403.1403.1405.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1409.1409.1409.1409.1409.1410.1414.1414.1414.1414.1462.1462.1462.1462.1462.1463.1466.1466.1466.1466.1466.1466.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: 17 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17.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 Creating DelPhi electrostatic grid real 1m50.353s user 0m26.170s sys 0m0.707s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m46.418s user 0m25.771s sys 0m0.647s Creating box around spheres Creating chemgrid maps real 0m38.005s user 0m11.078s sys 0m0.217s Atomic solvent excluded volume calculations underway FORTRAN STOP real 57m45.545s user 19m3.028s sys 0m0.059s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.