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 0m1.677s user 0m0.216s sys 0m0.457s 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 0:1236 spheres. 66. 66. 66. 66. 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. 75. 75. 84. 84. 84. 84. 86. 86. 86. 86. 87. 87. 87. 88. 88. 88. 88. 88. 88. 185. 199. 199. 199. 199. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 211. 211. 211. 211. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 214. 214. 214. 214. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 221. 221. 222. 222. 222. 223. 223. 224. 225. 230. 230. 230. 230. 230. 230. 231. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 240. 240. 240. 240. 240. 240. 240. 246. 246. 246. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 257. 257. 257. 257. 257. 260. 260. 260. 260. 261. 261. 263. 263. 263. 264. 264. 264. 264. 357. 360. 360. 360. 360. 361. 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991.1005.1005.1005.1005.1005.1005.1005.1012.1012.1107.1107.1108.1113.1113.1114.1114.1114.1118.1118.1118.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1148.1149.1149.1149.1149.1150.1150.1150.1152.1152.1152.1152.1152.1152.1157.1157.1157.1158.1158.1158.1158.1158.1158.1159.1160.1160.1161.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1164.1164.1164.1164.1164.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1167.1167.1167.1167.1167.1170.1172.1172.1172.1172.1172.1172.1172.1172.1184.1184.1184.1184.1184.1184.1204.1207.1207.1207.1207.1207.1207.1207.1208.1208.1208.1208.1208.1208.1208.1209.1209.1209.1209.1209.1209.1329.1329.1329.1329.1329.1329.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1345.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1361.1361.1361.1362.1362.1362.1362.1362.1363.1363.1367.1367.1367.1367.1367.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1379.1379.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1385.1385.1388.1388.1388.1392.1392.1392.1392.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1407.1407.1407.1407.1407.1407.1407.1407.1407.1407.1415.1415.1415.1415.1415.1415.1415.1421.1421.1421.1421.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1425.1425.1425.1425.1425.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.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: 39 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.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 0m26.366s user 0m23.599s sys 0m0.746s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m35.292s user 0m23.550s sys 0m0.700s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m21.841s user 0m8.620s sys 0m0.224s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m21.154s user 18m19.433s sys 0m0.093s 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.