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 0m4.988s user 0m0.919s sys 0m0.739s 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 0:1826 spheres. 63. 64. 64. 64. 64. 64. 64. 64. 64. 64. 64. 64. 64. 64. 70. 70. 70. 70. 70. 77. 81. 81. 81. 81. 81. 81. 81. 81. 81. 82. 82. 82. 82. 83. 83. 83. 84. 84. 84. 85. 85. 85. 85. 85. 85. 85. 85. 85. 86. 86. 86. 86. 87. 88. 91. 91. 91. 91. 91. 91. 91. 91. 93. 93. 93. 93. 93. 93. 93. 93. 93. 101. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 102. 103. 109. 109. 109. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 112. 113. 113. 113. 113. 113. 113. 113. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 118. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 119. 125. 125. 125. 125. 125. 125. 125. 125. 125. 125. 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746. 746. 747. 747. 747. 747. 750. 750. 750. 753. 753. 753. 754. 755. 755. 755. 755. 761. 761. 761. 761. 761. 763. 763. 763. 764. 765. 765. 765. 765. 765. 765. 765. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 768. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 770. 772. 772. 772. 772. 775. 775. 775. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 779. 782. 782. 784. 784. 784. 785. 785. 785. 785. 785. 785. 786. 786. 786. 786. 786. 786. 786. 786. 786. 786. 786. 786. 786. 786. 789. 790. 790. 790. 790. 790. 790. 791. 791. 791. 791. 791. 791. 791. 791. 791. 791. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 802. 804. 804. 804. 804. 804. 804. 804. 805. 805. 805. 805. 806. 806. 806. 806. 806. 806. 806. 806. 806. 806. 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950.1003.1003.1006.1006.1006.1006.1007.1007.1009.1009.1009.1009.1009.1015.1015.1015.1015.1015.1020.1020.1020.1020.1024.1024.1024.1024.1024.1024.1024.1024.1025.1032.1032.1032.1032.1032.1032.1032.1032.1033.1033.1033.1033.1033.1033.1034.1034.1034.1036.1039.1039.1039.1039.1039.1039.1039.1039.1039.1039.1039.1039.1039.1048.1050.1050.1050.1051.1071.1071.1071.1071.1071.1071.1071.1071.1072.1072.1072.1072.1072.1072.1072.1072.1072.1072.1072.1072.1074.1078.1078.1078.1078.1078.1078.1078.1078.1079.1079.1081.1081.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1082.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1083.1088.1088.1088.1088.1089.1089.1092.1092.1092.1092.1092.1092.1096.1096.1096.1096.1096.1096.1096.1096.1097.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1103.1103.1104.1104.1104.1104.1104.1104.1104.1106.1106.1106.1106.1106.1106.1106.1106.1106.1107.1107.1108.1108.1108.1108.1109.1111.1111.1112.1112.1112.1114.1114.1117.1117.1117.1121.1121.1122.1122.1122.1122.1122.1122.1125.1125.1125.1127.1128.1129.1129.1129.1129.1129.1129.1132.1132.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1140.1141.1141.1141.1141.1141.1142.1142.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1146.1146.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1153.1153.1153.1153.1153.1153.1153.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1164.1164.1164.1164.1164.1164.1164.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1174.1174.1174.1174.1174.1174.1174.1174.1174.1175.1175.1175.1175.1175.1175.1223.1223.1223.1223.1223.1223.1224.1224.1224.1228.1228.1228.1228.1228.1228.1229.1229.1229.1229.1229.1229.1229.1229.1229.1229.1229.1229.1230.1230.1230.1231.1231.3057.3057.3057.3057.3061.3061.3063.3068.3068.3068.3069.3070.3070.3070.3070.3070.3070.3070.3070.3070.3070.3070.3070.3070.3070.3076.3076.3077.3079.3079.3079.3079.3079.3079.3079.3080.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3081.3092.3092.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3093.3094.3094.3094.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3095.3096.3096.3096.3096.3096.3097.3097.3097.3097.3097.3097.3097.3097.3097.3097.3097.3097.3098.3098.3098.3099.3099.3099.3099.3099.3099.3099.3099.3103.3105.3105.3108.3108.3108.3108.3108.3108.3108.3108.3109.3109.3109.3110.3110.3110.3110.3110.3110.3119.3119.3119.3119.3121.3121.3121.3121.3121.3125.3125.3125.3125.3127.3128.3128.3128.3128.3128.3128.3128.3128.3128.3128.3129.3129.3129.3129.3129.3129.3129.3129.3129.3130.3130.3130.3130.3130.3130.3130.3130.3130.3130.3130.3130.3130.3130.3134.3134.3134.3134.3134.3134.3134.3134.3134.3134.3134.3134.3134.3135.3135.3135.3137.3137.3137.3137.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.3138.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: 33 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.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 were asked to cook * N * *GLH* 22 we had to cook * CA * we had to cook * C * we had to cook * O * we had to cook * CB * we had to cook * CG * we had to cook * CD * we had to cook * OE1* we had to cook * OE2* we had to cook * HN * we had to cook * HE2* we were asked to cook *ZN * * ZN* 22 Creating DelPhi electrostatic grid FORTRAN STOP mv: cannot stat `fort.14': No such file or directory real 0m33.897s user 0m31.499s sys 0m0.741s make: *** [grids/rec+sph.phi] Error 1