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 0m2.128s user 0m0.326s sys 0m0.277s 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 0:1531 spheres. 66. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 73. 74. 74. 81. 81. 82. 82. 82. 85. 85. 86. 86. 86. 86. 181. 181. 181. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 195. 195. 195. 195. 195. 195. 195. 195. 196. 196. 196. 196. 196. 196. 196. 196. 196. 196. 196. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 213. 213. 213. 213. 213. 217. 217. 218. 218. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 223. 223. 223. 225. 226. 226. 226. 226. 226. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 229. 229. 229. 230. 230. 230. 242. 242. 242. 242. 242. 242. 358. 358. 359. 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639. 639. 639. 639. 639. 654. 654. 654. 660. 660. 660. 660. 660. 661. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 664. 664. 664. 664. 664. 664. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 668. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 820. 820. 820. 820. 820. 820. 822. 823. 823. 824. 824. 824. 824. 824. 824. 825. 825. 825. 825. 827. 827. 827. 827. 827. 827. 836. 836. 836. 836. 839. 839. 839. 839. 839. 839. 840. 935. 935. 935. 949. 951. 951. 951. 951. 951. 951. 951. 951. 951. 951. 960. 960. 961. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 971. 973. 973. 973. 973. 973. 973. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 980. 980. 980. 980. 980. 980. 981. 981. 981. 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990.1003.1003.1003.1003.1003.1003.1003.1003.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1010.1011.1011.1011.1011.1011.1011.1011.1011.1011.1011.1012.1013.1013.1013.1013.1013.1014.1014.1014.1093.1093.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1099.1100.1100.1100.1101.1101.1101.1101.1102.1102.1102.1102.1102.1103.1104.1104.1104.1104.1104.1104.1104.1104.1104.1105.1105.1105.1105.1105.1109.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1121.1121.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1124.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1137.1137.1138.1138.1139.1140.1140.1140.1141.1141.1141.1141.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1149.1150.1150.1150.1150.1150.1150.1150.1153.1153.1153.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1164.1164.1164.1164.1166.1166.1166.1166.1168.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1171.1171.1171.1171.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1173.1173.1173.1173.1173.1173.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1177.1178.1178.1200.1200.1200.1200.1200.1214.1214.1214.1214.1214.1214.1214.1217.1217.1217.1217.1218.1218.1218.1218.1218.1317.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1322.1323.1323.1323.1323.1323.1323.1323.1323.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1338.1338.1338.1338.1353.1353.1353.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1365.1365.1365.1365.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1372.1372.1372.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1383.1385.1385.1385.1385.1385.1385.1385.1385.1392.1392.1392.1392.1392.1392.1392.1392.1392.1393.1393.1393.1393.1393.1393.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1415.1415.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1420.1420.1420.1420.1420.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.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: 59 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. 52. 53. 54. 55. 56. 57. 58. 59.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... Detecting missing residue atoms... 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 0m58.303s user 0m51.600s sys 0m2.221s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* we had to cook * HD2* Creating DelPhi electrostatic grid real 0m58.531s user 0m54.604s sys 0m2.548s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m32.355s user 1m31.019s sys 0m0.885s Atomic solvent excluded volume calculations underway FORTRAN STOP real 27m14.581s user 27m12.490s sys 0m0.161s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.